Filter results by: Taxon Proteome
1 - 50 of 7041 UniProtKB matches
(780 models, 15557 structures.)
UniProtKB AC
(Name)
UniProtKB Section
 
Homology Model
 
Experimental Structure
OrganismDescription
P0DTD3
(ORF9C_SARS2)
Swiss-ProtSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Putative ORF9c protein;
Uncharacterized protein 14;
P0DTD8
(NS7B_SARS2)
Swiss-ProtSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF7b protein;
Accessory protein 7b;
A0A663DJA2
(ORF10_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Putative ORF10 protein;
P0DTC7
(NS7A_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF7a protein;
Accessory protein 7a;
Protein U122;
Protein X4;
P0DTC9
(NCAP_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Nucleoprotein;
Nucleocapsid protein;
P0DTC2
(SPIKE_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
P0DTD1
(R1AB_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Replicase polyprotein 1ab;
ORF1ab polyprotein;
Host translation inhibitor nsp1;
Leader protein;
Non-structural protein 1;
nsp1;
Non-structural protein 2;
nsp2;
p65 homolog;
Papain-like protease nsp3;
3.4.19.12;
3.4.22.-;
Non-structural protein 3;
nsp3;
PL2-PRO;
Papain-like proteinase;
PL-PRO;
Non-structural protein 4;
nsp4;
3C-like proteinase nsp5;
3CL-PRO;
3CLp;
3.4.22.69;
Main protease;
Mpro;
Non-structural protein 5;
nsp5;
SARS coronavirus main proteinase;
Non-structural protein 6;
nsp6;
Non-structural protein 7;
nsp7;
Non-structural protein 8;
nsp8;
Viral protein genome-linked nsp9;
Non-structural protein 9;
nsp9;
RNA-capping enzyme subunit nsp9;
Non-structural protein 10;
nsp10;
Growth factor-like peptide;
GFL;
RNA-directed RNA polymerase nsp12;
Pol;
RdRp;
2.7.7.48;
2.7.7.50;
Non-structural protein 12;
nsp12;
Helicase nsp13;
Hel;
3.6.4.12;
3.6.4.13;
Non-structural protein 13;
nsp13;
Guanine-N7 methyltransferase nsp14;
2.1.1.56;
3.1.13.-;
Non-structural protein 14;
nsp14;
Proofreading exoribonuclease nsp14;
ExoN;
Uridylate-specific endoribonuclease nsp15;
4.6.1.-;
NendoU;
Non-structural protein 15;
nsp15;
2'-O-methyltransferase nsp16;
2.1.1.57;
Non-structural protein 16;
nsp16;
P0DTC3
(AP3A_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3a protein;
Accessory protein 3a;
Protein 3a;
Protein U274;
Protein X1;
P0DTC5
(VME1_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Membrane protein;
E1 glycoprotein;
Matrix glycoprotein;
Membrane glycoprotein;
P0DTG1
(ORF3C_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3c protein;
ORF3h protein;
P0DTG0
(ORF3D_SARS2)
Swiss-ProtSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Putative ORF3d protein;
P0DTF1
(ORF3B_SARS2)
Swiss-ProtSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Putative ORF3b protein;
P0DTC6
(NS6_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF6 protein;
Accessory protein 6;
Non-structural protein 6;
Protein X3;
P0DTC1
(R1A_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Replicase polyprotein 1a;
ORF1a polyprotein;
Host translation inhibitor nsp1;
Leader protein;
Non-structural protein 1;
nsp1;
Non-structural protein 2;
nsp2;
p65 homolog;
Papain-like protease nsp3;
3.4.19.12;
3.4.22.-;
Non-structural protein 3;
nsp3;
PL2-PRO;
Papain-like proteinase;
PL-PRO;
Non-structural protein 4;
nsp4;
3C-like proteinase nsp5;
3CL-PRO;
3CLp;
3.4.22.69;
Main protease;
Mpro;
Non-structural protein 5;
nsp5;
SARS coronavirus main proteinase;
Non-structural protein 6;
nsp6;
Non-structural protein 7;
nsp7;
Non-structural protein 8;
nsp8;
RNA-capping enzyme subunit nsp9;
Non-structural protein 9;
nsp9;
2.7.7.50;
Non-structural protein 10;
nsp10;
Growth factor-like peptide;
GFL;
Non-structural protein 11;
nsp11;
P0DTC8
(NS8_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF8 protein;
Non-structural protein 8;
P0DTD2
(ORF9B_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF9b protein;
Accessory protein 9b;
ORF-9b;
Protein 9b;
P0DTC4
(VEMP_SARS2)
Swiss-Prot
Severe acute respiratory syndrome coronavirus 2
(2019-nCoV)
Envelope small membrane protein;
A0A8B1JCK1
(A0A8B1JCK1_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF7a protein;
A0A8B1JCN7
(A0A8B1JCN7_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B1JG31
(A0A8B1JG31_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Envelope protein;
A0A8B1JMU0
(A0A8B1JMU0_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Envelope protein;
A0A8B6RAR4
(A0A8B6RAR4_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A8B6RMH4
(A0A8B6RMH4_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3a protein;
A0A8B6RMJ6
(A0A8B6RMJ6_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B1JQY8
(A0A8B1JQY8_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A7U3HM79
(A0A7U3HM79_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A899JGM5
(A0A899JGM5_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A8B1JI00
(A0A8B1JI00_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3a protein;
A0A8B1JVR7
(A0A8B1JVR7_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B1JEM1
(A0A8B1JEM1_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A8B6RCD2
(A0A8B6RCD2_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B6RKR4
(A0A8B6RKR4_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A6N1NLW7
(A0A6N1NLW7_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3a protein;
A0A7U3ECS3
(A0A7U3ECS3_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A859GR41
(A0A859GR41_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B1JLB2
(A0A8B1JLB2_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A8B1KNG9
(A0A8B1KNG9_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF8 protein;
A0A7U3EF41
(A0A7U3EF41_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Surface glycoprotein;
A0A8B1JL81
(A0A8B1JL81_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A8B6RVC4
(A0A8B6RVC4_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A6M8UDY5
(A0A6M8UDY5_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A859GUG0
(A0A859GUG0_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B1JYT8
(A0A8B1JYT8_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B1K0U6
(A0A8B1K0U6_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF8 protein;
A0A7U3HEZ3
(A0A7U3HEZ3_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Nucleoprotein;
A0A8B6RGA2
(A0A8B6RGA2_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
A0A7T5EC79
(A0A7T5EC79_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3a protein;
A0A8B1JQM9
(A0A8B1JQM9_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
ORF3a protein;
A0A8B1JWN1
(A0A8B1JWN1_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Accessory protein 7a;
A0A8B6RGF5
(A0A8B6RGF5_SARS2)
TrEMBLSevere acute respiratory syndrome coronavirus 2
(2019-nCoV)
Spike glycoprotein;
E2;
Peplomer protein;
Spike protein S1;
Spike protein S2;
Spike protein S2';
1 - 50 of 7041
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission.

"Severe acute respiratory syndrome coronavirus 2", Wikipedia: The Free Encyclopedia

We modelled the full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 which is identical to GenBank entry MN908947, and annotations from UniProt. The underlying SWISS-MODEL workspace projects are accessible below. Our colleagues at the Swiss Institute of Bioinformatics provide more resources on the SARS-CoV-2 genome on ViralZone or allow to track the current outbreak on Nextstrain. Several SARS-CoV-2 proteins reportedly interact in hetero-oligomeric complexes for which we also provide models in a dedicated hetero section. But be aware: the result of any theoretical modelling procedure is NON-EXPERIMENTAL and must be considered with care as models may contain significant errors. To this end SWISS-MODEL provides quality metrics which are described in the help section. The provided modelling projects are based on SWISS-MODEL template library version 2023-05-05 and will be updated as new templates become available.

IntAct lists interactions derived from literature curation or direct user submissions. We extracted those interactions and list the ones between SARS-CoV-2 and human host proteins with their structural coverage in a dedicated interaction page.

SARS-CoV-2 Variants of Concern were added as Annotation Projects to SWISS-MODEL Repository for Omicron variants 21K (BA.1), 21L (BA.2), 22A (BA.4), 22B (BA.5) and 22C (BA.2.12.1). Compare these variants on the spike protein, SPIKE_SARS2

Previously circulating Variants of Concern included Alpha, Beta, Delta and Gamma. Compare these variants on the spike protein, SPIKE_SARS2

Previously circulating Variants of Interest included Lambda and Mu. Compare these on the spike protein, SPIKE_SARS2

Show sequences
UniProtKB AC · Name
Description & Available Models
>sp|P0DTD1|R1AB_SARS2|1-7096
MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV
LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK
VLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG
AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVN
ITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEW
SMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPL
EFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVV
QTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATN
NAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQ
HEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVE
QKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDIN
GNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV
PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLA
HAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLINTLND
LNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEH
FIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVITFDNLKTLL
SLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYV
LPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNCYLATAL
LTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHAN
LDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQ
ESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYK
GPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPIDLVPNQPY
PNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVTFFPDLNGDVVAIDYKHYTPSFK
KGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLA
CEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILKPANNSLKITEEVGHTDLMAAYV
DNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTIANYAKPFLNKVVSTTTNIVTRC
LNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTIAKNTVKSVGKFCLEASFNYLKS
PNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLGMPSYCTGYREGYLNSTNVTIAT
YCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYV
LGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHV
VDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCA
GSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSH
FVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDV
GDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQG
FVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHIN
AQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIAL
KGGKIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDI
ASTDTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGD
FLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLE
GSVAYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVST
SGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL
AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDV
SFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAAL
CTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALND
FSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVY
CPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPK
TPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV
SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDR
WFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMN
GRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILTSLLVLVQSTQW
SLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV
MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGARRVWTLMNVLTLVYK
VYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIM
LVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLLPPKNSIDAFKL
NIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILL
AKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAIASEFSSLPSYAAFATA
QEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSED
KRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTY
KNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ
NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSD
GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEV
PANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQES
FGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYG
CSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKF
LKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDG
DMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVEN
PDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPG
SGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFK
YWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHF
RELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQ
TVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQ
LLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALF
AYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVV
IGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSL
SHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALL
STDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNS
TYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVY
LPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYI
RKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRC
GACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHK
PPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAE
TLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIG
EYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTL
NISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDA
LCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEI
SMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDM
FLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVV
REFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSC
NVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVI
TGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFIT
REEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSR
VSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSM
KYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQS
NHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHM
VVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSD
KFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSA
FVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYL
DAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIIN
NTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDY
KRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSV
KGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQ
MEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDF
IPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEIS
FMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMM
NVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLND
FVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLA
LGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGY
VMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLII
RENNRVVISSDVLVNN

Replicase polyprotein 1ab

Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.

Partial coverage by an experimental hetero-oligomeric complex (PDB: 8eir) is available and a high quality model can be extracted but should be used with care.

We model the mature proteins resulting from the cleavage and list them below.

>sp|P0DTD1|R1AB_SARS2|1-180
MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGV
LPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRK
VLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG

Host translation inhibitor nsp1

Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:33479166, PubMed:33080218, PubMed:32680882, PubMed:32908316). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:33080218, PubMed:32680882, PubMed:32979938). The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation (By similarity). This inhibits the integrated stress response (ISR) in the infected cell by preventing EIF2S1/eIF2-alpha phosphorylation upstream of stress granule formation and depletes host G3BP1 (PubMed:36534661). Viral mRNAs less susceptible to nsp1-mediated inhibition of translation, because of their 5'-end leader sequence (PubMed:32908316, PubMed:33080218).

Experimental structures (PDB: 7eq4, 7k3n, 7k7p, 8a4y, 8a55, 8aou, 8ays, 8az8, 8crf, 8crk, 8crm) are available. Experimental structures of hetero-oligomeric complexes (PDB: 6zlw, 6zm7, 6zme, 6zmi, 6zmo, 6zmt, 6zn5, 6zoj, 6zok, 6zon, 6zp4, 7jqb, 7jqc, 7k5i) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|181-818
AYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQLDFIDTKRGVYCCREHEHEIAW
YTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRI
RSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYL
PQNAVVKIYCPACHNSEVGPEHSLAEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKC
AYWVPRASANIGCNHTGVVGEGSEGLNDNLLEILQKEKVNINIVGDFKLNEEIAIILASF
SASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKSILSPLYAFASEA
ARVVRSIFSRTLETAQNSVRVLQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAY
ITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIV
GGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKC
VKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVG
TPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG

Non-structural protein 2 (nsp2)

Enhances mRNA repression of the 4EHP-GYF2 complex in the host, thereby inhibiting the antiviral response and facilitating SARS-CoV-2 replication. Possibly acts in cooperation with nsp1, which induces ribosome stalling on host mRNA, triggering mRNA repression by the host 4EHP-GYF2 complex which is enhanced by nsp2.

Experimental structures (PDB: 7exm, 7msw, 7msx) are available.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|819-2763
APTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEKCSAYTVELGTEVNEFACVVADA
VIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEE
EEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQ
TTTIQTIVEVQPQLEMELTPVVQTIEVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVV
NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVV
GPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF
DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEE
VTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA
VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPS
IISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDY
GARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVS
SPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYT
SNPTTFHLDGEVITFDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTY
LDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKY
PQVNGLTSIKWADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYC
NKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQ
FKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKH
ITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDN
YYKKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVT
FFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWSTKP
VETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGDIILK
PANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNSVPWDTI
ANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRIKASMPTTI
AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTAALGVLMSNLG
MPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLETIQITISSFKWDL
TAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWLMWLIINLVQMAPIS
AMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECTTIVNGVRRSFYVYA
NGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKN
GSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSAS
VYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEA
ELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYN
KVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNL
PFKLTCATTRQVVNVVTTKIALKGG

Papain-like protease nsp3

Responsible for the cleavages located at the N-terminus of the replicase polyprotein. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication (PubMed:35551511). Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3 (PubMed:32733001). Prevents also host NF-kappa-B signaling (By similarity). In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates (PubMed:32726803). Cleaves preferentially ISG15 from antiviral protein IFIH1 (MDA5), but not RIGI (PubMed:33727702). Can play a role in host ADP-ribosylation by ADP-ribose (PubMed:32578982). Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511).

Partial coverage by experimental structures (PDB: 5rs7, 5rs8, 5rs9, 5rsb, 5rsc, 5rsd, 5rse, 5rsf, 5rsg, 5rsh, 5rsi, 5rsj, 5rsk, 5rsl, 5rsm, 5rsn, 5rso, 5rsp, 5rsq, 5rsr, 5rss, 5rst, 5rsu, 5rsv, 5rsw, 5rsx, 5rsy, 5rsz, 5rt0, 5rt1, 5rt2, 5rt3, 5rt4, 5rt5, 5rt6, 5rt7, 5rt8, 5rt9, 5rta, 5rtb, 5rtc, 5rtd, 5rte, 5rtf, 5rtg, 5rth, 5rti, 5rtj, 5rtk, 5rtl, 5rtm, 5rtn, 5rto, 5rtp, 5rtq, 5rtr, 5rts, 5rtt, 5rtu, 5rtv, 5rtw, 5rtx, 5rty, 5rtz, 5ru0, 5ru1, 5ru2, 5ru3, 5ru4, 5ru5, 5ru6, 5ru7, 5ru8, 5ru9, 5rua, 5ruc, 5rud, 5rue, 5ruf, 5rug, 5ruh, 5rui, 5ruj, 5ruk, 5rul, 5rum, 5run, 5ruo, 5rup, 5ruq, 5rur, 5rus, 5rut, 5ruu, 5ruv, 5ruw, 5rux, 5ruy, 5ruz, 5rv0, 5rv1, 5rv2, 5rv3, 5rv4, 5rv5, 5rv6, 5rv7, 5rv8, 5rv9, 5rva, 5rvb, 5rvc, 5rvd, 5rve, 5rvf, 5rvg, 5rvh, 5rvi, 5rvj, 5rvk, 5rvl, 5rvm, 5rvn, 5rvo, 5rvp, 5rvq, 5rvr, 5rvs, 5rvt, 5rvu, 5rvv, 5s18, 5s1a, 5s1c, 5s1e, 5s1g, 5s1i, 5s1k, 5s1m, 5s1o, 5s1q, 5s1s, 5s1u, 5s1w, 5s1y, 5s20, 5s22, 5s24, 5s26, 5s27, 5s28, 5s29, 5s2a, 5s2b, 5s2c, 5s2d, 5s2e, 5s2f, 5s2g, 5s2h, 5s2i, 5s2j, 5s2k, 5s2l, 5s2m, 5s2n, 5s2o, 5s2p, 5s2q, 5s2r, 5s2s, 5s2t, 5s2u, 5s2v, 5s2w, 5s2x, 5s2y, 5s2z, 5s30, 5s31, 5s32, 5s33, 5s34, 5s35, 5s36, 5s37, 5s38, 5s39, 5s3a, 5s3b, 5s3c, 5s3d, 5s3e, 5s3f, 5s3g, 5s3h, 5s3i, 5s3j, 5s3k, 5s3l, 5s3m, 5s3n, 5s3o, 5s3p, 5s3q, 5s3r, 5s3s, 5s3t, 5s3u, 5s3v, 5s3w, 5s3x, 5s3y, 5s3z, 5s40, 5s41, 5s42, 5s43, 5s44, 5s45, 5s46, 5s47, 5s48, 5s49, 5s4a, 5s4b, 5s4c, 5s4d, 5s4e, 5s4f, 5s4g, 5s4h, 5s4i, 5s4j, 5s4k, 5s73, 5s74, 5soi, 5soj, 5sok, 5sol, 5som, 5son, 5soo, 5sop, 5soq, 5sor, 5sos, 5sot, 5sou, 5sov, 5sow, 5sox, 5soy, 5soz, 5sp0, 5sp1, 5sp2, 5sp3, 5sp4, 5sp6, 5sp7, 5sp8, 5sp9, 5spa, 5spb, 5spc, 5spd, 5spe, 5spf, 5spg, 5sph, 5spi, 5spj, 5spk, 5spl, 5spm, 5spn, 5spo, 5spp, 5spq, 5spr, 5sps, 5spt, 5spu, 5spv, 5spw, 5spx, 5spy, 5spz, 5sq0, 5sq1, 5sq2, 5sq3, 5sq4, 5sq5, 5sq6, 5sq7, 5sq8, 5sq9, 5sqa, 5sqb, 5sqc, 5sqd, 5sqe, 5sqf, 5sqg, 5sqh, 5sqi, 5sqj, 5sqk, 5sql, 5sqm, 5sqn, 5sqo, 5sqp, 5sqq, 5sqr, 5sqs, 5sqt, 5squ, 5sqv, 5sqw, 5sqx, 5sqy, 5sqz, 5sr0, 5sr1, 5sr2, 5sr3, 5sr4, 5sr5, 5sr6, 5sr7, 5sr8, 5sr9, 5sra, 5srb, 5src, 5srd, 5sre, 5srf, 5srg, 5srh, 5sri, 5srj, 5srk, 5srl, 5srm, 5srn, 5sro, 5srp, 5srq, 5srr, 5srs, 5srt, 5sru, 5srv, 5srw, 5srx, 5sry, 5srz, 5ss0, 5ss1, 5ss2, 5ss3, 5ss4, 5ss5, 5ss6, 5ss7, 5ss8, 5ss9, 5ssa, 5ssb, 5ssc, 5ssd, 5sse, 5ssf, 5ssg, 5ssh, 5ssi, 5ssj, 5ssk, 5ssl, 5ssm, 5ssn, 5sso, 5ssp, 5ssq, 5ssr, 6vxs, 6w02, 6w6y, 6w9c, 6wcf, 6wen, 6wey, 6woj, 6wrh, 6wuu, 6wx4, 6wzu, 6xg3, 6ywk, 6ywl, 6ywm, 6z5t, 6z6i, 6z72, 7bf3, 7bf4, 7bf5, 7bf6, 7c33, 7cjd, 7cjm, 7cmd, 7cz4, 7d47, 7d6h, 7d7k, 7d7l, 7e35, 7fr0, 7fr1, 7fr2, 7fr3, 7fr4, 7fr5, 7fr6, 7fr7, 7fr8, 7fr9, 7fra, 7frb, 7frc, 7frd, 7gyy, 7gyz, 7gz0, 7gz1, 7gz2, 7gz3, 7gz4, 7gz5, 7gz6, 7gz7, 7gz8, 7gz9, 7gza, 7gzb, 7gzc, 7gzd, 7gze, 7gzf, 7gzg, 7gzh, 7gzi, 7gzj, 7gzk, 7gzl, 7gzm, 7gzn, 7gzo, 7gzq, 7gzr, 7gzs, 7gzt, 7gzu, 7gzv, 7gzw, 7gzx, 7gzy, 7gzz, 7h00, 7h01, 7h02, 7h03, 7h04, 7h05, 7h06, 7h07, 7h08, 7h09, 7h0a, 7h0b, 7h0c, 7h0d, 7h0e, 7h0f, 7h0g, 7h0h, 7h0i, 7h0j, 7h0k, 7h0l, 7h0m, 7h0n, 7h0o, 7h0p, 7h0q, 7h0r, 7h0s, 7h0t, 7h0u, 7h0v, 7h0w, 7h0x, 7h0y, 7h0z, 7h10, 7h11, 7h12, 7h13, 7h14, 7h15, 7h16, 7h17, 7h18, 7h19, 7h1a, 7h1b, 7h1c, 7h1d, 7h1e, 7h1f, 7h1g, 7jir, 7jit, 7jiv, 7jiw, 7jme, 7jn2, 7jrn, 7kag, 7kg3, 7koj, 7kok, 7kol, 7kqo, 7kqp, 7kqw, 7kr0, 7kr1, 7krx, 7kxb, 7lbr, 7lbs, 7lg7, 7lgo, 7llf, 7llz, 7los, 7m1y, 7nfv, 7nt4, 7ofs, 7oft, 7ofu, 7p2o, 7qcg, 7qch, 7qci, 7qcj, 7qck, 7qcm, 7qg7, 7rqg, 7rzc, 7sdr, 7sgu, 7sgv, 7sgw, 7sqe, 7t9w, 7thh, 7ti9, 7twf, 7twg, 7twh, 7twi, 7twj, 7twn, 7two, 7twp, 7twq, 7twr, 7tws, 7twt, 7twv, 7tww, 7twx, 7twy, 7tx0, 7tx1, 7tx3, 7tx4, 7tx5, 7tzj, 7xc3, 7xc4, 7ybg, 8azc, 8azd, 8azi, 8azl, 8azm, 8azn, 8azo, 8azp, 8c19, 8c1a, 8ers, 8eua, 8f2e, 8fwn, 8fwo, 8g62, 8gia, 8gqc, 8hbl, 8hda, 8iho, 8ilc, 8sh6, 8sh8, 8tv6, 8tv7, 8ufm, 8uob, 8uuf, 8uug, 8uuh, 8uuu, 8uuv, 8uuw, 8uuy, 8uvm, 8vec, 8xab, 9azx) is available. Partial coverage by experimental structures of hetero-oligomeric complexes exist (PDB: 6xa9, 6xaa, 6yva, 7pku, 7rbr, 7rbs, 7uv5, 7wzo, 8cx9) and high quality models can be extracted from them but should be used with care.

High quality models are available that cover various stretches of the target sequence.

>sp|P0DTD1|R1AB_SARS2|2764-3263
KIVNNWLKQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIAST
DTCFANKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLH
FLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSV
AYESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSGR
WVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYY
FMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFL
AHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFEEAALCTF
LLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHLAKALNDFSN
SGSDVLYQPPQTSITSAVLQ

Non-structural protein 4 (nsp4)

Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511).

High quality models are available for the C-terminus which are predicted to form homo-dimers.

>sp|P0DTD1|R1AB_SARS2|3264-3569
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIR
KSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNG
SPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGN
FYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYE
PLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

3C-like proteinase nsp5 (3CL-PRO)

Cleaves the C-terminus of replicase polyprotein at 11 sites (PubMed:32321856). Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN] (PubMed:32198291, PubMed:32272481). May cleave human NLRP1 in lung epithelial cells, thereby activating the NLRP1 inflammasome pathway (PubMed:35594856). May cleave human GSDMD, triggering alternative GSDME-mediated epithelial cell death upon activation of the NLRP1 inflammasome, which may enhance the release interleukins 1B, 6, 16 and 18 (PubMed:35594856). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (PubMed:32198291, PubMed:32272481).

Experimental structures (PDB: 5r7y, 5r7z, 5r80, 5r81, 5r82, 5r83, 5r84, 5r8t, 5re4, 5re5, 5re6, 5re7, 5re8, 5re9, 5rea, 5reb, 5rec, 5red, 5ree, 5ref, 5reg, 5reh, 5rei, 5rej, 5rek, 5rel, 5rem, 5ren, 5reo, 5rep, 5rer, 5res, 5ret, 5reu, 5rev, 5rew, 5rex, 5rey, 5rez, 5rf0, 5rf1, 5rf2, 5rf3, 5rf4, 5rf5, 5rf6, 5rf7, 5rf8, 5rf9, 5rfa, 5rfb, 5rfc, 5rfd, 5rfe, 5rff, 5rfg, 5rfh, 5rfi, 5rfj, 5rfk, 5rfl, 5rfm, 5rfn, 5rfo, 5rfp, 5rfq, 5rfr, 5rfs, 5rft, 5rfu, 5rfv, 5rfw, 5rfx, 5rfy, 5rfz, 5rg0, 5rg1, 5rg2, 5rg3, 5rgg, 5rgh, 5rgi, 5rgj, 5rgk, 5rgl, 5rgm, 5rgn, 5rgo, 5rgp, 5rgq, 5rgr, 5rgs, 5rgt, 5rgu, 5rgv, 5rgw, 5rgx, 5rgy, 5rgz, 5rh0, 5rh1, 5rh2, 5rh3, 5rh4, 5rh5, 5rh6, 5rh7, 5rh8, 5rh9, 5rha, 5rhb, 5rhc, 5rhd, 5rhe, 5rhf, 5rl0, 5rl1, 5rl2, 5rl3, 5rl4, 5rl5, 5sml, 5smm, 5smn, 6lu7, 6lze, 6m03, 6m0k, 6m2n, 6m2q, 6w63, 6w79, 6wnp, 6wqf, 6wtj, 6wtk, 6wtm, 6wtt, 6xa4, 6xb0, 6xb1, 6xb2, 6xbg, 6xbh, 6xbi, 6xch, 6xfn, 6xhm, 6xhu, 6xkf, 6xkh, 6xmk, 6xoa, 6xqs, 6xqt, 6xqu, 6xr3, 6y2e, 6y2f, 6y2g, 6y84, 6yb7, 6ynq, 6yvf, 6z2e, 6zrt, 6zru, 7a1u, 7abu, 7adw, 7aeg, 7aeh, 7af0, 7aga, 7aha, 7ak4, 7aku, 7alh, 7ali, 7amj, 7ans, 7aol, 7ap6, 7aph, 7aqe, 7aqi, 7aqj, 7ar5, 7ar6, 7arf, 7au4, 7avd, 7awr, 7aws, 7awu, 7aww, 7ax6, 7axm, 7axo, 7ay7, 7b2j, 7b2u, 7b3e, 7b5z, 7b77, 7b83, 7baj, 7bak, 7bal, 7bb2, 7be7, 7bfb, 7bgp, 7bij, 7bqy, 7bro, 7brp, 7buy, 7c2q, 7c2y, 7c6s, 7c6u, 7c7p, 7c8b, 7c8r, 7c8t, 7c8u, 7ca8, 7cam, 7cb7, 7cbt, 7com, 7cut, 7cuu, 7cwb, 7cwc, 7cx9, 7d1m, 7d1o, 7d3i, 7d64, 7dat, 7dau, 7dav, 7ddc, 7dg6, 7dgb, 7dgf, 7dgg, 7dgh, 7dgi, 7dhj, 7djr, 7dk1, 7dpp, 7dpu, 7dpv, 7e18, 7e19, 7e5x, 7e6k, 7ein, 7en8, 7en9, 7fay, 7faz, 7gav, 7gaw, 7gax, 7gay, 7gaz, 7gb0, 7gb1, 7gb2, 7gb3, 7gb4, 7gb5, 7gb6, 7gb7, 7gb8, 7gb9, 7gba, 7gbb, 7gbc, 7gbd, 7gbe, 7gbf, 7gbg, 7gbh, 7gbi, 7gbj, 7gbk, 7gbl, 7gbm, 7gbn, 7gbo, 7gbp, 7gbq, 7gbr, 7gbs, 7gbt, 7gbu, 7gbv, 7gbw, 7gbx, 7gby, 7gbz, 7gc0, 7gc1, 7gc2, 7gc3, 7gc4, 7gc5, 7gc6, 7gc7, 7gc8, 7gc9, 7gca, 7gcb, 7gcc, 7gcd, 7gce, 7gcf, 7gcg, 7gci, 7gcj, 7gck, 7gcl, 7gcm, 7gcn, 7gco, 7gcp, 7gcq, 7gcr, 7gcs, 7gct, 7gcu, 7gcv, 7gcw, 7gcx, 7gcy, 7gcz, 7gd0, 7gd1, 7gd2, 7gd3, 7gd4, 7gd5, 7gd6, 7gd7, 7gd8, 7gd9, 7gda, 7gdb, 7gdc, 7gdd, 7gde, 7gdf, 7gdg, 7gdh, 7gdi, 7gdj, 7gdk, 7gdl, 7gdm, 7gdn, 7gdo, 7gdp, 7gdq, 7gdr, 7gds, 7gdt, 7gdu, 7gdv, 7gdw, 7gdx, 7gdy, 7gdz, 7ge0, 7ge1, 7ge2, 7ge3, 7ge4, 7ge5, 7ge6, 7ge7, 7ge8, 7ge9, 7gea, 7geb, 7gec, 7ged, 7gee, 7gef, 7geg, 7geh, 7gei, 7gej, 7gek, 7gel, 7gem, 7gen, 7geo, 7geq, 7ger, 7ges, 7get, 7geu, 7gev, 7gew, 7gex, 7gey, 7gez, 7gf0, 7gf1, 7gf2, 7gf3, 7gf4, 7gf5, 7gf6, 7gf7, 7gf8, 7gf9, 7gfa, 7gfb, 7gfc, 7gfd, 7gfe, 7gff, 7gfg, 7gfh, 7gfi, 7gfj, 7gfk, 7gfl, 7gfm, 7gfn, 7gfo, 7gfp, 7gfq, 7gfr, 7gfs, 7gft, 7gfu, 7gfv, 7gfw, 7gfx, 7gfy, 7gfz, 7gg0, 7gg1, 7gg2, 7gg3, 7gg4, 7gg5, 7gg6, 7gg7, 7gg8, 7gg9, 7gga, 7ggb, 7ggc, 7ggd, 7gge, 7ggf, 7ggg, 7ggh, 7ggi, 7ggj, 7ggk, 7ggl, 7ggm, 7ggn, 7ggo, 7ggp, 7ggq, 7ggr, 7ggs, 7ggt, 7ggu, 7ggv, 7ggw, 7ggx, 7ggy, 7ggz, 7gh0, 7gh1, 7gh2, 7gh3, 7gh4, 7gh5, 7gh6, 7gh7, 7gh8, 7gh9, 7gha, 7ghb, 7ghc, 7ghd, 7ghe, 7ghf, 7ghg, 7ghh, 7ghi, 7ghj, 7ghk, 7ghl, 7ghm, 7ghn, 7gho, 7ghp, 7ghq, 7ghr, 7ghs, 7ght, 7ghu, 7ghv, 7ghw, 7ghx, 7ghy, 7ghz, 7gi0, 7gi1, 7gi2, 7gi3, 7gi4, 7gi5, 7gi6, 7gi7, 7gi8, 7gi9, 7gia, 7gib, 7gic, 7gid, 7gie, 7gif, 7gig, 7gih, 7gii, 7gij, 7gik, 7gil, 7gim, 7gin, 7gio, 7gip, 7giq, 7gir, 7gis, 7git, 7giu, 7giv, 7giw, 7gix, 7giy, 7giz, 7gj0, 7gj1, 7gj2, 7gj3, 7gj4, 7gj5, 7gj6, 7gj7, 7gj8, 7gj9, 7gja, 7gjb, 7gjc, 7gjd, 7gje, 7gjf, 7gjg, 7gjh, 7gji, 7gjj, 7gjk, 7gjl, 7gjm, 7gjn, 7gjo, 7gjp, 7gjq, 7gjr, 7gjs, 7gjt, 7gju, 7gjv, 7gjw, 7gjx, 7gjy, 7gjz, 7gk0, 7gk1, 7gk2, 7gk3, 7gk4, 7gk5, 7gk6, 7gk7, 7gk8, 7gk9, 7gka, 7gkb, 7gkc, 7gkd, 7gke, 7gkf, 7gkg, 7gkh, 7gki, 7gkj, 7gkk, 7gkl, 7gkm, 7gkn, 7gko, 7gkp, 7gkq, 7gkr, 7gks, 7gkt, 7gku, 7gkv, 7gkw, 7gkx, 7gky, 7gkz, 7gl0, 7gl1, 7gl2, 7gl3, 7gl4, 7gl5, 7gl6, 7gl7, 7gl8, 7gl9, 7gla, 7glb, 7glc, 7gld, 7gle, 7glf, 7glg, 7glh, 7gli, 7glj, 7glk, 7gll, 7glm, 7gln, 7glo, 7glp, 7glq, 7glr, 7gls, 7glt, 7glu, 7glv, 7glw, 7glx, 7gly, 7glz, 7gm0, 7gm1, 7gm2, 7gm3, 7gm4, 7gm5, 7gm6, 7gm7, 7gm8, 7gm9, 7gma, 7gmb, 7gmc, 7gmd, 7gme, 7gmf, 7gmg, 7gmh, 7gmi, 7gmj, 7gmk, 7gml, 7gmm, 7gmn, 7gmo, 7gmp, 7gmq, 7gmr, 7gms, 7gmt, 7gmu, 7gmv, 7gmw, 7gmx, 7gmy, 7gmz, 7gn0, 7gn1, 7gn2, 7gn3, 7gn4, 7gn5, 7gn6, 7gn7, 7gn8, 7gn9, 7gna, 7gnb, 7gnc, 7gnd, 7gne, 7gnf, 7gng, 7gnh, 7gni, 7gnj, 7gnk, 7gnl, 7gnm, 7gnn, 7gno, 7gnp, 7gnq, 7gnr, 7gns, 7gnt, 7gnu, 7gre, 7grf, 7grg, 7grh, 7gri, 7grj, 7grk, 7grl, 7grm, 7grn, 7gro, 7grp, 7grq, 7grr, 7grs, 7grt, 7gru, 7grv, 7grw, 7grx, 7gry, 7grz, 7gs0, 7gs1, 7gs2, 7gs3, 7gs4, 7gs5, 7gs6, 7jfq, 7jkv, 7joy, 7jp0, 7jp1, 7jpy, 7jpz, 7jq0, 7jq1, 7jq2, 7jq3, 7jq4, 7jq5, 7jr3, 7jr4, 7jst, 7jsu, 7jt0, 7jt7, 7ju7, 7jun, 7jvz, 7jw8, 7jyc, 7k0e, 7k0f, 7k3t, 7k40, 7k6d, 7k6e, 7kfi, 7khp, 7kph, 7kvl, 7kvr, 7kx5, 7kyu, 7l0d, 7l10, 7l11, 7l12, 7l13, 7l14, 7l5d, 7l8i, 7l8j, 7lb7, 7lbn, 7lco, 7lcr, 7lcs, 7lct, 7ldl, 7ldx, 7lfe, 7lfp, 7lkd, 7lke, 7lkr, 7lks, 7lkt, 7lku, 7lkv, 7lkw, 7lkx, 7lmd, 7lme, 7lmf, 7ltj, 7ltn, 7lyh, 7lyi, 7lzt, 7lzu, 7lzv, 7lzw, 7lzx, 7lzy, 7lzz, 7m00, 7m01, 7m02, 7m03, 7m04, 7m2p, 7m8m, 7m8n, 7m8o, 7m8p, 7m8x, 7m8y, 7m8z, 7m90, 7m91, 7mat, 7mau, 7mav, 7maw, 7max, 7maz, 7mb0, 7mb1, 7mb2, 7mb3, 7mbg, 7mbi, 7mhf, 7mhg, 7mhh, 7mhi, 7mhj, 7mhk, 7mhl, 7mhm, 7mhn, 7mho, 7mhp, 7mhq, 7mlf, 7mlg, 7mng, 7mpb, 7mrr, 7n44, 7n5z, 7n8c, 7nbr, 7nbs, 7nbt, 7nby, 7neo, 7nev, 7nf5, 7ng3, 7ng6, 7nij, 7nt1, 7nt2, 7nt3, 7ntq, 7nts, 7ntt, 7ntv, 7ntw, 7nuk, 7nw2, 7nwx, 7nxh, 7o46, 7p2g, 7p35, 7p51, 7pfl, 7pfm, 7phz, 7pxz, 7pzq, 7q5e, 7q5f, 7qbb, 7qka, 7ql8, 7qt5, 7qt6, 7qt7, 7qt8, 7r7h, 7rbz, 7rc0, 7rfr, 7rfs, 7rfu, 7rfw, 7rls, 7rm2, 7rmb, 7rme, 7rmt, 7rmz, 7rn0, 7rn1, 7rn4, 7rnh, 7rnk, 7rnw, 7rvm, 7rvn, 7rvo, 7rvp, 7rvq, 7rvr, 7rvs, 7rvt, 7rvu, 7rvv, 7rvw, 7rvx, 7rvy, 7rvz, 7rw0, 7rw1, 7s3k, 7s3s, 7s4b, 7s6w, 7s6x, 7s6y, 7s6z, 7s70, 7s71, 7s72, 7s73, 7s74, 7s75, 7s82, 7sd9, 7sda, 7sdc, 7set, 7sf1, 7sf3, 7sfb, 7sfh, 7sfi, 7sgh, 7sh7, 7sh8, 7sh9, 7si9, 7t2t, 7t2v, 7t42, 7t43, 7t44, 7t45, 7t46, 7t48, 7t49, 7t4a, 7t4b, 7tdu, 7te0, 7teh, 7tek, 7tel, 7tfr, 7tgr, 7tia, 7tiu, 7tiv, 7tiw, 7tix, 7tiy, 7tiz, 7tj0, 7tll, 7tob, 7tq2, 7tq3, 7tq4, 7tq5, 7tq6, 7tuu, 7tvx, 7u28, 7u29, 7u92, 7uj9, 7ujg, 7uju, 7ukk, 7ur9, 7urb, 7us4, 7uu6, 7uu7, 7uu8, 7uu9, 7uua, 7uub, 7uuc, 7uud, 7uue, 7uug, 7uup, 7v1t, 7v7m, 7vah, 7vfa, 7vfb, 7vh8, 7vic, 7vjw, 7vjx, 7vjy, 7vjz, 7vk0, 7vk1, 7vk2, 7vk3, 7vk4, 7vk5, 7vk6, 7vk7, 7vk8, 7vlp, 7vlq, 7vth, 7vu6, 7vvp, 7vvt, 7w9g, 7whc, 7wo1, 7wo2, 7wo3, 7wof, 7woh, 7wq8, 7wq9, 7wqa, 7wqb, 7wqk, 7wym, 7wyp, 7x6j, 7x6k, 7xar, 7xb3, 7xb4, 7xq6, 7xq7, 7xrs, 7z0p, 7z2k, 7z3u, 7z4s, 7z59, 7zb6, 7zb7, 7zb8, 7zqv, 7zv5, 7zv7, 7zv8, 8a4q, 8a4t, 8acd, 8acl, 8aeb, 8b0s, 8b0t, 8b2t, 8bfo, 8bfq, 8bga, 8bgd, 8bs1, 8bs2, 8c9l, 8c9o, 8cdc, 8cyu, 8cyz, 8cz4, 8cz7, 8czw, 8czx, 8d4j, 8d4k, 8d4l, 8d4m, 8d4n, 8d4p, 8dcz, 8dd1, 8dd6, 8dd9, 8ddi, 8ddm, 8dfe, 8dfn, 8dgb, 8di3, 8dib, 8dic, 8did, 8die, 8dif, 8dig, 8dih, 8dii, 8djj, 8dk8, 8dkh, 8dkj, 8dkk, 8dkl, 8dkz, 8dl9, 8dlb, 8dmd, 8dmn, 8dox, 8doy, 8dpr, 8drr, 8drs, 8drt, 8dru, 8drv, 8drw, 8drx, 8dry, 8drz, 8ds0, 8ds1, 8ds2, 8dsu, 8dt9, 8dz0, 8dz1, 8dz2, 8dz6, 8dz9, 8dza, 8dzb, 8dzc, 8e1y, 8e25, 8e26, 8e4j, 8e4r, 8e4w, 8e5c, 8e5x, 8e5z, 8e61, 8e63, 8e64, 8e65, 8e68, 8e69, 8e6a, 8ehj, 8ehk, 8ehl, 8ehm, 8ej7, 8ej9, 8eke, 8eoy, 8ey2, 8eyj, 8ezv, 8ezz, 8f02, 8f2c, 8f2d, 8f44, 8f45, 8f46, 8fig, 8fiv, 8fiw, 8ftc, 8ftl, 8fy6, 8fy7, 8gfk, 8gfn, 8gfo, 8gfr, 8gfu, 8gqt, 8gtv, 8gtw, 8gvd, 8gvy, 8gw4, 8gwj, 8gws, 8gxg, 8gxh, 8gxi, 8gzb, 8h3g, 8h3k, 8h3l, 8h4y, 8h51, 8h57, 8h5f, 8h5p, 8h6i, 8h6n, 8h7w, 8h82, 8hbk, 8hef, 8hht, 8hhu, 8hi9, 8hol, 8hom, 8hoz, 8hqf, 8hqg, 8hqh, 8hqi, 8hqj, 8htv, 8hur, 8huv, 8huw, 8hux, 8hvk, 8hvl, 8hvm, 8hvn, 8hvo, 8hvu, 8hvv, 8hvw, 8hvx, 8hvy, 8hvz, 8hzr, 8i30, 8i4s, 8ifp, 8ifq, 8ifr, 8ifs, 8ift, 8ig4, 8ig7, 8ig8, 8ig9, 8iga, 8igb, 8ign, 8igo, 8igx, 8igy, 8inq, 8int, 8inu, 8inw, 8inx, 8iny, 8j32, 8j35, 8j36, 8j37, 8j38, 8j39, 8j3a, 8j3b, 8jcj, 8jck, 8jcl, 8jcm, 8jcn, 8jco, 8jop, 8jpq, 8okb, 8okc, 8okk, 8okl, 8okm, 8okn, 8p54, 8p55, 8p56, 8p57, 8p58, 8p5a, 8p5b, 8p5c, 8p86, 8p87, 8ph4, 8r0v, 8r11, 8r12, 8r14, 8r16, 8r19, 8s9z, 8sg6, 8sk4, 8skh, 8spj, 8sty, 8stz, 8sxo, 8sxr, 8tbe, 8tpb, 8tpc, 8tpd, 8tpg, 8tph, 8tpi, 8uab, 8uh5, 8uh8, 8uh9, 8uho, 8uia, 8uif, 8ups, 8upv, 8upw, 8ur9, 8ute, 8v4u, 8vsg, 8wzp, 8wzq, 8ya5, 8ysa, 9arq, 9ars, 9art, 9avq, 9epl, 9epm) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7dvp, 7dvw, 7dvx, 7dvy, 7dw0, 7dw6, 7lmc, 7mb4, 7mb5, 7mb6, 7mb7, 7mb8, 7mb9, 7mgr, 7mgs, 7n6n, 7n89, 7t2u, 7t70, 7t8m, 7t8r, 7t9y, 7ta4, 7ta7, 7tb2, 7tbt, 7tc4, 7x6y, 8d35, 8ddl, 8eir, 8h7k) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|3570-3859
SAVKRTIKGTHHWLLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFV
KHKHAFLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAV
VLLILMTARTVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVT
TVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLG
VYDYLVSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQ

Non-structural protein 6 (nsp6)

Plays a role in the formation and maintenance of double membrane vesicles (DMVs) replication organelles (PubMed:35551511). DMVs are formed by nsp3 and nsp4, while nsp6 zippers ER membranes and connects to lipid droplets (PubMed:35551511). LDs are consumed during DMV formation (PubMed:35551511). Binds to host TBK1 without affecting TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).

Only remote homologues were identified as potential template structures, no models have been built.

See here for template search results.

>sp|P0DTD1|R1AB_SARS2|3860-3942
SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLL
SMQGAVDINKLCEEMLDNRATLQ

Non-structural protein 7 (nsp7)

Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, PubMed:32438371, PubMed:32526208). Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers (By similarity).

An experimental structure (PDB: 7lhq) is available. Experimental structures of hetero-oligomeric complexes (PDB: 6m5i, 6m71, 6wiq, 6wqd, 6wtc, 6xez, 6xip, 6xqb, 6yhu, 6yyt, 7aap, 7b3b, 7b3c, 7b3d, 7btf, 7bv1, 7bv2, 7bw4, 7bzf, 7c2k, 7ctt, 7cxm, 7cxn, 7cyq, 7d4f, 7dcd, 7dfg, 7dfh, 7doi, 7dok, 7dte, 7egq, 7eiz, 7jlt, 7krn, 7kro, 7krp, 7l1f, 7lg3, 7mb7, 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm, 7uo4, 7uo7, 7uo9, 7uob, 7uoe, 8gw1, 8gwb, 8gwe, 8gwf, 8gwg, 8gwi, 8gwk, 8gwm, 8gwn, 8gwo, 8gy6, 8sq9, 8sqj, 8sqk) exist and high quality models can be extracted from them but should be used with care.

>sp|P0DTD1|R1AB_SARS2|3943-4140
AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLE
KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNII
PLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNL
AWPLIVTALRANSAVKLQ

Non-structural protein 8 (nsp8)

Plays a role in viral RNA synthesis (PubMed:32358203, PubMed:32277040, PubMed:32438371, PubMed:32526208). Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers (By similarity). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP9, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).

Partial coverage by an experimental structure (PDB: 7ywr) is available. Experimental structures of hetero-oligomeric complexes (PDB: 6m5i, 6m71, 6wiq, 6wqd, 6wtc, 6xez, 6xip, 6xqb, 6yhu, 6yyt, 7aap, 7b3b, 7b3c, 7b3d, 7btf, 7bv1, 7bv2, 7bw4, 7bzf, 7c2k, 7ctt, 7cxm, 7cxn, 7cyq, 7d4f, 7dcd, 7dfg, 7dfh, 7doi, 7dok, 7dte, 7ed5, 7egq, 7eiz, 7jlt, 7krn, 7kro, 7krp, 7l1f, 7lg2, 7lmc, 7mb4, 7mb8, 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm, 7uo4, 7uo7, 7uo9, 7uob, 7uoe, 7x70, 8gw1, 8gwb, 8gwe, 8gwf, 8gwg, 8gwi, 8gwk, 8gwm, 8gwn, 8gwo, 8gy6, 8sq9, 8sqj, 8sqk) exist and high quality models can be extracted from them but should be used with care.

>sp|P0DTD1|R1AB_SARS2|4141-4253
NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSD
GTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ

Viral protein genome-linked nsp9

Forms a primer, NSP9-pU, which is utilized by the polymerase for the initiation of RNA chains (PubMed:37794589). Interacts with ribosome signal recognition particle RNA (SRP) (PubMed:33080218). Together with NSP8, suppress protein integration into the cell membrane, thereby disrupting host immune defenses (PubMed:33080218).

Experimental structures (PDB: 6w4b, 6w9q, 6wc1, 6wxd, 7bwq, 7kri, 7n3k, 8dqu) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7cyq, 7egq, 7eiz, 7thm, 8gw1, 8gwb, 8gwe, 8gwf, 8gwg, 8gwi, 8gwk, 8gwm, 8gwn, 8gwo, 8sq9, 8sqj, 8sqk) exist and high quality models can be extracted from them but should be used with care.

High quality models are available which are predicted to form homo-dimers.

>sp|P0DTD1|R1AB_SARS2|4254-4392
AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPE
ANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVC
GMWKGYGCSCDQLREPMLQ

Non-structural protein 10 (nsp10)

Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease (By similarity) and nsp16 2'-O-methyltransferase activities (PubMed:35944563). Therefore plays an essential role in viral mRNAs cap methylation.

Experimental structures (PDB: 6zct, 6zpe, 7orr, 7oru, 7orv, 7orw, 8bzn) are available. Experimental structures of hetero-oligomeric complexes (PDB: 6w4h, 6w61, 6w75, 6wjt, 6wkq, 6wks, 6wq3, 6wrz, 6wvn, 6xkm, 6yz1, 7bq7, 7c2i, 7c2j, 7diy, 7egq, 7eiz, 7jhe, 7jib, 7jpe, 7jyy, 7jz0, 7koa, 7l6r, 7l6t, 7lw3, 7lw4, 7mb9, 7mc5, 7mc6, 7n0b, 7n0c, 7n0d, 7r1t, 7r1u, 7ult, 8a23, 8bsd, 8bzv, 8c5m, 8f4s, 8f4y, 8osx, 8ot0, 8oto, 8otr, 8ov1, 8ov2, 8ov3, 8ov4, 8rv4, 8rv5, 8rv6, 8rv7, 8rv8, 8rv9, 8rva, 8rvb, 8rzc, 8rzd, 8rze, 8s8w, 8s8x, 8tyj, 9emj, 9eml, 9emv, 9eun) exist and high quality models can be extracted from them but should be used with care.

High quality models are available which are predicted to form homo-dodecamers.

>sp|P0DTD1|R1AB_SARS2|4393-5324
SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKD
EDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLT
KYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGE
RVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL
LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVN
CLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN
LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFY
DFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF
DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTIT
QMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHN
MLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECA
QVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV
RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIK
NFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGA
GCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHML
DMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ

RNA-directed RNA polymerase nsp12 (Pol)

RNA-directed RNA polymerase that catalyzes the transcription of viral genomic and subgenomic RNAs. Acts in complex with nsp7 and nsp8 to transcribe both the minus and positive strands of genomic RNA (PubMed:32277040, PubMed:32358203, PubMed:32438371, PubMed:32526208). The kinase-like NiRAN domain of NSP12 attaches one or more nucleotides to the amino terminus of NSP9, forming a covalent RNA-protein intermediate that serves as transcription/replication primer (PubMed:37794589). Subgenomic RNAs (sgRNAs) are formed by discontinuous transcription: The polymerase has the ability to pause at transcription-regulating sequences (TRS) and jump to the leader TRS, resulting in a major deletion (PubMed:35706445). This creates a series of subgenomic RNAs that are replicated, transcribed and translated (PubMed:35706445). In addition, Nsp12 is a subunit of the viral RNA capping enzyme that catalyzes the RNA guanylyltransferase reaction for genomic and sub-genomic RNAs (PubMed:35944563). Subsequently, the NiRAN domain transfers RNA to GDP, and forms the core cap structure GpppA-RNA (PubMed:35944563).

Experimental structures of hetero-oligomeric complexes (PDB: 6m71, 6xez, 6xqb, 6yyt, 7aap, 7b3b, 7b3c, 7b3d, 7btf, 7bv1, 7bv2, 7bw4, 7bzf, 7c2k, 7ctt, 7cxm, 7cxn, 7cyq, 7d4f, 7dfg, 7dfh, 7doi, 7dok, 7dte, 7ed5, 7egq, 7eiz, 7krn, 7kro, 7krp, 7l1f, 7o7y, 7o7z, 7o80, 7o81, 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm, 7uo4, 7uo7, 7uo9, 7uob, 7uoe, 8gw1, 8gwb, 8gwe, 8gwf, 8gwg, 8gwi, 8gwk, 8gwm, 8gwn, 8gwo, 8gy6, 8sq9, 8sqj, 8sqk) exist and high quality models can be extracted from them but should be used with care.

>sp|P0DTD1|R1AB_SARS2|5325-5925
AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDV
TQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDY
ILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPPLNRNY
VFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL
VPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYP
SARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTV
NALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPE
YFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVI
THDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSE
YDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATL
Q

Helicase nsp13 (Hel)

Plays a role in viral RNA synthesis (PubMed:33232691). Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium (By similarity). Binds to host TBK1 and inhibits TBK1 phosphorylation; the interaction with TBK1 decreases IRF3 phosphorylation, which leads to reduced IFN-beta production (PubMed:32979938).

Experimental structures (PDB: 5rl6, 5rl7, 5rl8, 5rl9, 5rlb, 5rlc, 5rld, 5rle, 5rlf, 5rlg, 5rlh, 5rli, 5rlj, 5rlk, 5rll, 5rlm, 5rln, 5rlo, 5rlp, 5rlq, 5rlr, 5rls, 5rlt, 5rlu, 5rlv, 5rlw, 5rly, 5rlz, 5rm0, 5rm1, 5rm2, 5rm3, 5rm4, 5rm5, 5rm6, 5rm7, 5rm8, 5rm9, 5rma, 5rmb, 5rmc, 5rmd, 5rme, 5rmf, 5rmg, 5rmh, 5rmi, 5rmj, 5rmk, 5rml, 5rmm, 5rob, 6zsl, 7nio, 7nn0, 7nng) are available. Experimental structures of hetero-oligomeric complexes (PDB: 6xez, 7cxm, 7cxn, 7cyq, 7egq, 7eiz, 7krn, 7kro, 7lfz, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 8gw1, 8gwb, 8gwe, 8gwf, 8gwg, 8gwi, 8gwk, 8gwm, 8gwn, 8gwo) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|5926-6452
AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGF
KMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAV
PTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDR
VVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPF
MIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIG
DELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKA
YKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLY
VNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG
GAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Guanine-N7 methyltransferase nsp14

Plays a role in viral RNA synthesis through two distinct activities. The N7-guanine methyltransferase activity plays a role in the formation of the cap structure GpppA-RNA (PubMed:35944563). The proofreading exoribonuclease reduces the sensitivity of the virus to RNA mutagens during replication (By similarity). This activity acts on both ssRNA and dsRNA in a 3'-5' direction (By similarity).

Experimental structures (PDB: 5skw, 5skx, 5sky, 5skz, 5sl0, 5sl1, 5sl2, 5sl3, 5sl4, 5sl5, 5sl6, 5sl7, 5sl8, 5sl9, 5sla, 5slb, 5slc, 5sld, 5sle, 5slf, 5slg, 5slh, 5sli, 5slj, 5slk, 5sll, 5slm, 5sln, 5slo, 5slp, 5slq, 5slr, 5sls, 5slt, 5slu, 5slv, 5slw, 5slx, 5sly, 5slz, 5sm0, 5sm1, 5sm2, 5sm3, 5sm4, 5sm5, 5sm6, 5sm7, 5sm8, 5sm9, 5sma, 5smb, 5smc, 5smd, 5sme, 5smf, 5smg, 5smh, 5smi, 5smk, 7qgi, 7qif, 7r2v, 7tw7, 7tw8, 7tw9, 8bwu, 8frj, 8frk) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7diy, 7egq, 7eiz, 7mc5, 7mc6, 7n0b, 7n0c, 7n0d, 8cmg) exist and high quality models can be extracted from them but should be used with care.

High quality models can be extracted from hetero-oligomeric complexes but should be used with care.

>sp|P0DTD1|R1AB_SARS2|6453-6798
SLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAK
RNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLT
VFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYK
KVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDF
SHSQLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLD
DFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQ

Uridylate-specific endoribonuclease nsp15

Plays a role in viral transcription/replication and prevents the simultaneous activation of host cell dsRNA sensors, such as MDA5/IFIH1, OAS, and PKR (By similarity). Acts by degrading the 5'-polyuridines generated during replication of the poly(A) region of viral genomic and subgenomic RNAs (PubMed:33504779, PubMed:33564093). Catalyzes a two-step reaction in which a 2'3'-cyclic phosphate (2'3'-cP) is first generated by 2'-O transesterification, which is then hydrolyzed to a 3'-phosphate (3'-P) (PubMed:33504779, PubMed:33564093). If not degraded, poly(U) RNA would hybridize with poly(A) RNA tails and activate host dsRNA sensors (By similarity). May bind genomic dsRNA in association with the replication-transcription complex (RTC), and play a role in nsp12 discontinous transcription (PubMed:34562452, PubMed:35706445).

Experimental structures (PDB: 5s6x, 5s6y, 5s6z, 5s70, 5s71, 5s72, 5sa4, 5sa5, 5sa6, 5sa7, 5sa8, 5sa9, 5saa, 5sab, 5sac, 5sad, 5sae, 5saf, 5sag, 5sah, 5sai, 5sbf, 6vww, 6w01, 6wlc, 6wxc, 6x1b, 6x4i, 6xdh, 7k0r, 7k1l, 7k1o, 7k9p, 7keg, 7keh, 7kf4, 7me0, 7n06, 7n33, 7n7r, 7n7u, 7n7w, 7n7y, 7n83, 7rb0, 7rb2, 7tj2, 7tqv, 8d34, 8u2x, 8ud2, 8ud3, 8ud4, 8ud5) are available.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|6799-7096
SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLA
VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHT
ANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADL
YKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

2'-O-methyltransferase nsp16

Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs (PubMed:35944563). N7-methyl guanosine cap is a prerequisite for binding of nsp16 (PubMed:35944563). Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system (PubMed:35944563). May disrupt host mRNA splicing in nucleus by interacting with pre-mRNA Recognition Domains ofthe U1 and U2 snRNAs (PubMed:33080218).

Experimental structures of hetero-oligomeric complexes (PDB: 6w4h, 6w61, 6w75, 6wjt, 6wkq, 6wks, 6wq3, 6wrz, 6wvn, 6xkm, 6yz1, 7bq7, 7c2i, 7c2j, 7jhe, 7jib, 7jpe, 7jyy, 7jz0, 7koa, 7l6r, 7l6t, 7lw3, 7lw4, 7r1t, 7r1u, 7ult, 8a23, 8bsd, 8bzv, 8c5m, 8f4s, 8f4y, 8osx, 8ot0, 8oto, 8otr, 8ov1, 8ov2, 8ov3, 8ov4, 8rv4, 8rv5, 8rv6, 8rv7, 8rv8, 8rv9, 8rva, 8rvb, 8rzc, 8rzd, 8rze, 8s8w, 8s8x, 8tyj, 9emj, 9eml, 9emv, 9eun) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

P0DTC2 · SPIKE_SARS2
(1273 residues)
>sp|P0DTC2|SPIKE_SARS2
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYT

Spike glycoprotein (S glycoprotein)

Spike protein S1 (14-685): Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. The major receptor is host ACE2 (PubMed:32142651, PubMed:33607086, PubMed:32155444). When S2/S2' has been cleaved, binding to the receptor triggers direct fusion at the cell membrane (PubMed:34561887). When S2/S2' has not been cleaved, binding to the receptor results in internalization of the virus by endocytosis leading to fusion of the virion membrane with the host endosomal membrane (PubMed:32221306, PubMed:32075877). Alternatively, may use NRP1/NRP2 (PubMed:33082294, PubMed:33082293) and integrin as entry receptors (PubMed:35150743). The use of NRP1/NRP2 receptors may explain the tropism of the virus in human olfactory epithelial cells, which express these molecules at high levels but ACE2 at low levels (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Spike protein S2 (686-1273): Precursor of the fusion protein processed in the biosynthesis of the S protein and the formation of virus particle. Mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. Contains two viral fusion peptides that are unmasked after cleavage. The S2/S2' cleavage occurs during virus entry at the cell membrane by host TMPRSS2 (PubMed:32142651) or during endocytosis by host CSTL (PubMed:32703818, PubMed:34159616). In either case, this triggers an extensive and irreversible conformational change leading to fusion of the viral envelope with the cellular cytoplasmic membrane, releasing viral genomic RNA into the host cell cytoplasm (PubMed:34561887). Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of the viral and target cell membranes, the coiled coil regions (heptad repeats) adopt a trimer-of-hairpins structure and position the fusion peptide in close proximity to the C-terminal region of the ectodomain. Formation of this structure appears to promote apposition and subsequent fusion of viral and target cell membranes. Spike protein S2' (816-1273): Subunit of the fusion protein that is processed upon entry into the host cell. Mediates fusion of the virion and cellular membranes by functioning as a class I viral fusion protein. Contains a viral fusion peptide that is unmasked after S2 cleavage. This cleavage can occur at the cell membrane by host TMPRSS2 or during endocytosis by host CSTL (PubMed:32703818, PubMed:34159616). In either case, this triggers an extensive and irreversible conformational change that leads to fusion of the viral envelope with the cellular cytoplasmic membrane, releasing viral genomic RNA into the host cell cytoplasm (PubMed:34561887). Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During fusion of the viral and target cell membranes, the coiled coil regions (heptad repeats) adopt a trimer-of-hairpins structure and position the fusion peptide in close proximity to the C-terminal region of the ectodomain. Formation of this structure appears to promote apposition and subsequent fusion of viral and target cell membranes.

Experimental structures (PDB: 6lvn, 6vsb, 6vxx, 6vyb, 6w41, 6wps, 6wpt, 6x29, 6x2a, 6x2b, 6x2c, 6x6p, 6x79, 6xc2, 6xc3, 6xc4, 6xc7, 6xcm, 6xcn, 6xdg, 6xe1, 6xf5, 6xf6, 6xkl, 6xkp, 6xkq, 6xlu, 6xm0, 6xm3, 6xm4, 6xm5, 6xr8, 6xra, 6xs6, 6yla, 6ym0, 6yor, 6yz5, 6yz7, 6z2m, 6z43, 6z97, 6zb4, 6zb5, 6zbp, 6zcz, 6zdg, 6zdh, 6zer, 6zfo, 6zge, 6zgg, 6zgh, 6zgi, 6zh9, 6zhd, 6zlr, 6zow, 6zox, 6zoy, 6zoz, 6zp0, 6zp1, 6zp2, 6zp5, 6zp7, 6zwv, 6zxn, 7a25, 7a29, 7a4n, 7a5r, 7a5s, 7a93, 7ad1, 7akd, 7b14, 7b17, 7b18, 7b27, 7b3o, 7b62, 7beh, 7bei, 7bej, 7bek, 7bel, 7bem, 7ben, 7beo, 7bep, 7bnm, 7bnn, 7bno, 7bnv, 7bwj, 7byr, 7bz5, 7c01, 7c2l, 7c8v, 7c8w, 7cab, 7cac, 7cah, 7cai, 7cak, 7can, 7cdi, 7cdj, 7ch4, 7ch5, 7chb, 7chc, 7che, 7chf, 7chh, 7cho, 7chp, 7chs, 7cjf, 7cm4, 7cn9, 7cwl, 7cwm, 7cwn, 7cwo, 7cws, 7cwt, 7cwu, 7cyh, 7cyp, 7cyv, 7d0b, 7d0c, 7d0d, 7d2z, 7d30, 7d4g, 7d6i, 7dcc, 7dcx, 7dd2, 7dd8, 7ddd, 7ddn, 7deo, 7det, 7deu, 7df3, 7dhx, 7djz, 7dk0, 7dk2, 7dk3, 7dk4, 7dk5, 7dk6, 7dk7, 7dpm, 7dwy, 7dwz, 7dx0, 7dx1, 7dx2, 7dx3, 7dzw, 7dzx, 7dzy, 7e23, 7e39, 7e3b, 7e3c, 7e3j, 7e3k, 7e3l, 7e3o, 7e5o, 7e5r, 7e5s, 7e5y, 7e7b, 7e7d, 7e7x, 7e7y, 7e86, 7e88, 7e8c, 7e8m, 7e9n, 7e9o, 7e9p, 7e9q, 7e9t, 7eam, 7ean, 7eaz, 7eb0, 7eb3, 7eb4, 7eb5, 7edf, 7edg, 7edh, 7edi, 7eh5, 7ej4, 7ej5, 7ejy, 7ejz, 7ek0, 7enf, 7eng, 7epx, 7ey0, 7ey5, 7ezv, 7f0x, 7f12, 7f15, 7f3q, 7f46, 7f5g, 7f5h, 7f62, 7f63, 7f6y, 7f6z, 7f7e, 7f7h, 7fae, 7faf, 7fat, 7fau, 7fb0, 7fb1, 7fb3, 7fb4, 7fbj, 7fbk, 7fcd, 7fce, 7fcp, 7fcq, 7fet, 7fg2, 7fg3, 7fg7, 7fjc, 7fjn, 7fjo, 7fjs, 7jji, 7jjj, 7jmo, 7jmp, 7jmw, 7jv2, 7jv4, 7jv6, 7jva, 7jvb, 7jvc, 7jw0, 7jwb, 7jwy, 7jx3, 7jzl, 7jzm, 7jzn, 7jzu, 7k43, 7k45, 7k4n, 7k8m, 7k8s, 7k8t, 7k8u, 7k8v, 7k8w, 7k8x, 7k8y, 7k8z, 7k90, 7k9h, 7k9i, 7k9j, 7k9k, 7k9z, 7kdg, 7kdh, 7kdi, 7kdj, 7kdk, 7kdl, 7ke4, 7ke6, 7ke7, 7ke8, 7ke9, 7kea, 7keb, 7kec, 7kfv, 7kfw, 7kfx, 7kfy, 7kgj, 7kgk, 7kj5, 7kkk, 7kkl, 7kl9, 7klg, 7klh, 7klw, 7km5, 7kmg, 7kmh, 7kmi, 7kmk, 7kml, 7kn3, 7kn4, 7kn5, 7kn6, 7kn7, 7kqb, 7kqe, 7krq, 7krr, 7krs, 7ks9, 7ksg, 7kxj, 7kxk, 7kzb, 7l02, 7l06, 7l09, 7l2c, 7l2d, 7l2e, 7l2f, 7l3n, 7l4z, 7l56, 7l57, 7l58, 7l5b, 7l7d, 7l7e, 7l7k, 7laa, 7lab, 7lc8, 7lcn, 7ld1, 7ldj, 7ljr, 7lm8, 7lop, 7lq7, 7lqv, 7lqw, 7lrs, 7lrt, 7ls9, 7lss, 7lwi, 7lwj, 7lwk, 7lwl, 7lwm, 7lwn, 7lwo, 7lwp, 7lwq, 7lws, 7lwt, 7lwu, 7lwv, 7lww, 7lx5, 7lxw, 7lxx, 7lxy, 7lxz, 7ly0, 7ly2, 7ly3, 7lyk, 7lyl, 7lym, 7lyn, 7lyo, 7lyp, 7lyq, 7m0j, 7m3i, 7m42, 7m53, 7m6d, 7m6e, 7m6f, 7m6g, 7m6h, 7m6i, 7m71, 7m7b, 7m7w, 7m8j, 7m8k, 7mdw, 7me7, 7mej, 7mf1, 7mfu, 7mjg, 7mjh, 7mji, 7mjj, 7mjk, 7mjl, 7mkl, 7mkm, 7mlz, 7mm0, 7mmo, 7msq, 7mtc, 7mtd, 7mte, 7mw2, 7mw3, 7mw4, 7mw5, 7mw6, 7mxp, 7my2, 7my3, 7my8, 7mzf, 7mzg, 7mzh, 7mzi, 7mzj, 7mzk, 7mzl, 7mzm, 7mzn, 7n0g, 7n0h, 7n1q, 7n1t, 7n1u, 7n1v, 7n1w, 7n1x, 7n1y, 7n3i, 7n4i, 7n4j, 7n4l, 7n4m, 7n5h, 7n62, 7n64, 7n8h, 7n8i, 7n9a, 7n9b, 7n9c, 7n9e, 7n9t, 7nab, 7nd3, 7nd4, 7nd5, 7nd6, 7nd7, 7nd8, 7nd9, 7nda, 7ndb, 7ndc, 7ndd, 7neg, 7neh, 7nkt, 7nll, 7np1, 7ns6, 7nt9, 7nta, 7ntc, 7nx6, 7nx7, 7nx8, 7nx9, 7nxa, 7nxb, 7oan, 7oao, 7oap, 7oaq, 7oau, 7oay, 7od3, 7odl, 7olz, 7or9, 7ora, 7orb, 7owx, 7p40, 7p5g, 7p5q, 7p5s, 7p77, 7p78, 7p79, 7p7a, 7p7b, 7phg, 7pqy, 7pqz, 7pr0, 7pry, 7prz, 7ps0, 7ps1, 7ps2, 7ps4, 7ps5, 7ps6, 7ps7, 7q0a, 7q0g, 7q0h, 7q0i, 7q1z, 7q3q, 7q3r, 7q6e, 7q9f, 7q9g, 7q9i, 7q9j, 7q9k, 7q9m, 7q9p, 7qdg, 7qdh, 7qez, 7qf0, 7qf1, 7qnw, 7qnx, 7qny, 7qo7, 7qo9, 7qti, 7qtj, 7qtk, 7qur, 7qus, 7r13, 7r14, 7r15, 7r16, 7r17, 7r18, 7r19, 7r1b, 7r40, 7r4i, 7r4q, 7r4r, 7r6w, 7r6x, 7r7n, 7r8l, 7r8m, 7r8n, 7r8o, 7r95, 7ra8, 7ral, 7raq, 7rbv, 7rby, 7rku, 7rkv, 7rnj, 7rq6, 7rr0, 7ru1, 7ru2, 7ru3, 7ru4, 7ru5, 7ru8, 7rw2, 7s0b, 7s0c, 7s0d, 7s0e, 7s3n, 7s4s, 7s5p, 7s5q, 7s5r, 7s6i, 7s6j, 7s6k, 7s6l, 7s83, 7sbk, 7sbl, 7sbo, 7sbp, 7sbq, 7sbr, 7sbs, 7sbt, 7sbu, 7sc1, 7sd5, 7si2, 7sj0, 7sjs, 7skz, 7sl5, 7sn2, 7sn3, 7so9, 7soa, 7sob, 7soc, 7sod, 7soe, 7sof, 7spo, 7spp, 7swn, 7swo, 7swp, 7sww, 7swx, 7sxr, 7sxs, 7sxt, 7sxu, 7sxv, 7sxw, 7t01, 7t3m, 7t67, 7t72, 7t7b, 7t9j, 7tas, 7tat, 7tb4, 7tb8, 7tbf, 7tca, 7tcc, 7tei, 7tey, 7tf1, 7tf2, 7tf3, 7tf4, 7tf5, 7tf8, 7tge, 7tgw, 7tgx, 7tgy, 7the, 7thk, 7tht, 7tl1, 7tl9, 7tla, 7tlb, 7tlc, 7tld, 7tly, 7tm0, 7tnw, 7to4, 7tou, 7tov, 7tow, 7tox, 7toy, 7toz, 7tp0, 7tp1, 7tp2, 7tp3, 7tp4, 7tp7, 7tp8, 7tp9, 7tpa, 7tpc, 7tpe, 7tpf, 7tph, 7tpi, 7tpk, 7tpl, 7tpr, 7tyz, 7tz0, 7u09, 7u0a, 7u0d, 7u0e, 7u0p, 7u0q, 7u0x, 7u2d, 7u2e, 7u8e, 7u9o, 7u9p, 7uap, 7uaq, 7uar, 7ub0, 7ub5, 7ub6, 7uhc, 7ukl, 7ukm, 7ul0, 7upl, 7urq, 7urs, 7uz4, 7uz5, 7uz6, 7uz7, 7uz8, 7uz9, 7uza, 7uzb, 7uzc, 7uzd, 7v20, 7v22, 7v23, 7v24, 7v26, 7v27, 7v2a, 7v76, 7v77, 7v78, 7v79, 7v7a, 7v7d, 7v7e, 7v7f, 7v7g, 7v7h, 7v7i, 7v7j, 7v7n, 7v7o, 7v7p, 7v7q, 7v7r, 7v7s, 7v7t, 7v7u, 7v7v, 7v8c, 7vhh, 7vhj, 7vhk, 7vhl, 7vhm, 7vhn, 7vmu, 7vnb, 7vnc, 7vnd, 7vne, 7voa, 7vq0, 7vrv, 7vrw, 7vx1, 7vxe, 7vxi, 7vyr, 7vzt, 7w1s, 7w92, 7w94, 7w9e, 7w9f, 7wb5, 7wbz, 7wcd, 7wch, 7wck, 7wcp, 7wcr, 7wcu, 7wcz, 7wd0, 7wd1, 7wd2, 7wd7, 7wd8, 7wd9, 7wdf, 7we7, 7we8, 7we9, 7wea, 7web, 7wec, 7wed, 7wee, 7wef, 7wev, 7wg6, 7wg7, 7wg8, 7wg9, 7wgv, 7wgx, 7wgy, 7wgz, 7wh8, 7whb, 7whd, 7whi, 7whj, 7whk, 7wjy, 7wjz, 7wk0, 7wk2, 7wk3, 7wk8, 7wk9, 7wka, 7wlc, 7wly, 7wlz, 7wm0, 7wn2, 7wnb, 7wo4, 7wo5, 7wo7, 7woa, 7wob, 7woc, 7wog, 7wop, 7woq, 7wor, 7wos, 7wou, 7wov, 7wow, 7wp6, 7wp8, 7wp9, 7wpd, 7wpe, 7wpf, 7wph, 7wqv, 7wr8, 7wrj, 7wrv, 7ws0, 7ws1, 7ws2, 7ws3, 7ws4, 7ws5, 7ws6, 7ws7, 7wt7, 7wt8, 7wt9, 7wtf, 7wtg, 7wth, 7wti, 7wtj, 7wtk, 7wue, 7wuh, 7wvl, 7wwi, 7wwj, 7wwk, 7wwl, 7wwm, 7wz1, 7wz2, 7x1m, 7x2h, 7x2k, 7x2l, 7x2m, 7x63, 7x66, 7x6a, 7x7d, 7x7e, 7x7n, 7x7o, 7x7t, 7x7u, 7x8w, 7x8y, 7x8z, 7x90, 7x91, 7x92, 7x93, 7x94, 7x95, 7x96, 7x9e, 7xck, 7xco, 7xcz, 7xd2, 7xda, 7xdb, 7xdk, 7xdl, 7xeg, 7xei, 7xh8, 7xic, 7xik, 7xil, 7xiw, 7xix, 7xiy, 7xiz, 7xj6, 7xj8, 7xj9, 7xmx, 7xmz, 7xnq, 7xnr, 7xns, 7xod, 7xs8, 7xsa, 7xsb, 7xsc, 7xst, 7xtz, 7xu0, 7xu1, 7xu2, 7xu3, 7xu4, 7xu5, 7xu6, 7xy3, 7xy4, 7y0c, 7y0n, 7y0o, 7y0v, 7y3o, 7y42, 7y6d, 7y6k, 7y6l, 7y6n, 7y7j, 7y7k, 7y9s, 7yad, 7ybh, 7ybi, 7ybj, 7ybk, 7ybl, 7ybm, 7ybn, 7yc5, 7yck, 7ycl, 7ycn, 7yco, 7yd1, 7ydy, 7ye5, 7ye9, 7yh6, 7yh7, 7ykj, 7yow, 7yqt, 7yqu, 7yqv, 7yqw, 7yqx, 7yqy, 7yqz, 7yr0, 7yr1, 7ytn, 7yue, 7yve, 7yvf, 7yvg, 7yvh, 7yvi, 7yvj, 7yvk, 7yvl, 7yvm, 7yvn, 7yvo, 7yvp, 7z0x, 7z0y, 7z1a, 7z1b, 7z1c, 7z1d, 7z1e, 7z3z, 7z6v, 7z7x, 7z85, 7z86, 7z8o, 7z9q, 7z9r, 7zbu, 7zce, 7zcf, 7zf3, 7zf4, 7zf5, 7zf8, 7zf9, 7zfa, 7zfb, 7zfc, 7zfd, 7zfe, 7zjl, 7zr7, 7zr8, 7zr9, 7zrc, 7zxu, 8a99, 8aaa, 8bbn, 8bcz, 8be1, 8bec, 8bev, 8bg2, 8bg3, 8bg4, 8bg5, 8bg6, 8bg8, 8bgg, 8bh5, 8bon, 8bse, 8bsf, 8c1v, 8c3v, 8c8p, 8cbd, 8cbe, 8cbf, 8cim, 8cin, 8cma, 8csa, 8csj, 8cwi, 8cwu, 8cwv, 8cxn, 8cxq, 8cy6, 8cy7, 8cy9, 8cya, 8cyb, 8cyc, 8cyd, 8cyj, 8d0z, 8d36, 8d47, 8d48, 8d55, 8d56, 8d5a, 8d6z, 8d8q, 8d8r, 8dad, 8dcc, 8dce, 8dgu, 8di5, 8dli, 8dll, 8dlo, 8dlr, 8dls, 8dlt, 8dlw, 8dlx, 8dly, 8dlz, 8dm0, 8dm1, 8dm2, 8dm3, 8dm4, 8dnn, 8dpz, 8dt3, 8dt8, 8dtk, 8dtr, 8dtt, 8dtx, 8dw2, 8dw3, 8dw9, 8dwa, 8dxs, 8dxt, 8dxu, 8dya, 8dzh, 8dzi, 8e1g, 8el2, 8elj, 8elo, 8elp, 8elq, 8eoo, 8epn, 8epp, 8epq, 8eqf, 8erq, 8err, 8eyg, 8eyh, 8f0g, 8f0h, 8f0i, 8f2j, 8f2x, 8f4p, 8fah, 8fez, 8fhy, 8fi9, 8fu7, 8fu8, 8fu9, 8g70, 8g71, 8g72, 8g73, 8g74, 8g75, 8g76, 8g77, 8g78, 8g79, 8g7a, 8g7b, 8g7c, 8gb0, 8gb5, 8gb6, 8gb7, 8gb8, 8gdr, 8gf2, 8gjm, 8gjn, 8gnh, 8gou, 8gpy, 8gs6, 8gs9, 8gsb, 8gto, 8gtp, 8gtq, 8gx9, 8gz5, 8gzz, 8h00, 8h01, 8h07, 8h08, 8h3d, 8h3e, 8h3m, 8h3n, 8h5t, 8h5u, 8h6f, 8h7l, 8h7z, 8h91, 8hc2, 8hc3, 8hc4, 8hc5, 8hc8, 8hc9, 8hca, 8hcb, 8heb, 8hec, 8hed, 8hes, 8hgl, 8hgm, 8hhx, 8hhy, 8hhz, 8hn6, 8hn7, 8hp9, 8hpf, 8hpq, 8hpu, 8hpv, 8hq7, 8hr2, 8hrd, 8hri, 8hrj, 8hws, 8hwt, 8i3s, 8i3u, 8i4e, 8i4f, 8i4g, 8i4h, 8i5h, 8i5i, 8idn, 8ios, 8iot, 8itu, 8iv4, 8iv5, 8iv8, 8iva, 8ix3, 8j1q, 8j1t, 8j1v, 8j26, 8jyk, 8jym, 8k3k, 8k45, 8k46, 8k47, 8k5g, 8k5h, 8khc, 8khd, 8owt, 8owv, 8oww, 8oyu, 8p99, 8p9y, 8pq2, 8psd, 8q7s, 8q93, 8q94, 8q95, 8qpr, 8qq0, 8qrf, 8qrg, 8qtd, 8qzr, 8r1c, 8r80, 8r8k, 8sdf, 8sdg, 8sgu, 8siq, 8sir, 8sis, 8sit, 8sk5, 8smi, 8smt, 8suo, 8t21, 8tm1, 8tma, 8tyl, 8tyo, 8u1g, 8u28, 8uul, 8uum, 8uun, 8uuo, 8vkk, 8vye, 8vyf, 8vyg, 8wlo, 8wlr, 8wmd, 8wmf, 8xe9, 8xea, 8xi6, 8zby, 8zbz, 8zc0, 8zc1, 8zc3, 8zc4, 8zc5) are available. Experimental structures of hetero-oligomeric complexes (PDB: 6lzg, 6m0j, 6m17, 6vw1, 6x45, 6xey, 7a91, 7a92, 7a94, 7a95, 7a96, 7a97, 7a98, 7b0b, 7bh9, 7c8d, 7c8j, 7ct5, 7czp, 7czq, 7czr, 7czs, 7czt, 7czu, 7czv, 7czw, 7czx, 7czy, 7czz, 7d00, 7d03, 7df4, 7dmu, 7dqa, 7dwx, 7dx4, 7dx5, 7dx6, 7dx7, 7dx8, 7dx9, 7e8f, 7edj, 7efp, 7efr, 7ek6, 7ekc, 7eke, 7ekf, 7ekg, 7ekh, 7ey4, 7eya, 7f5r, 7fc5, 7fdg, 7fdh, 7fdi, 7fdk, 7fem, 7kj2, 7kj3, 7kj4, 7kmb, 7kms, 7kmz, 7knb, 7kne, 7knh, 7kni, 7l0n, 7l7f, 7lo4, 7mjm, 7mjn, 7nxc, 7p19, 7r0z, 7r10, 7r11, 7r12, 7r1a, 7rbu, 7rpv, 7rxd, 7rzq, 7rzr, 7rzs, 7rzt, 7rzu, 7rzv, 7sn0, 7sxx, 7sxy, 7sxz, 7sy0, 7sy1, 7sy2, 7sy3, 7sy4, 7sy5, 7sy6, 7sy7, 7sy8, 7t9k, 7t9l, 7tew, 7tex, 7tez, 7tf0, 7tik, 7tn0, 7u0n, 7ufk, 7ufl, 7v7z, 7v80, 7v81, 7v82, 7v83, 7v84, 7v85, 7v86, 7v87, 7v88, 7v89, 7v8a, 7v8b, 7vx4, 7vx5, 7vx9, 7vxa, 7vxb, 7vxc, 7vxd, 7vxf, 7vxk, 7vxm, 7w6u, 7w8s, 7w99, 7w9b, 7w9c, 7wa1, 7wbl, 7wbp, 7wbq, 7wgb, 7wgc, 7whh, 7whz, 7wk4, 7wk5, 7wk6, 7wnm, 7won, 7wp0, 7wp1, 7wp2, 7wp5, 7wpa, 7wpb, 7wpc, 7wrh, 7wri, 7ws8, 7ws9, 7wsa, 7wse, 7wsh, 7wsk, 7wvp, 7wvq, 7xa7, 7xaz, 7xb0, 7xb1, 7xby, 7xch, 7xci, 7xcp, 7xid, 7xo4, 7xo5, 7xo6, 7xo7, 7xo8, 7xo9, 7xoa, 7xob, 7xoc, 7xrp, 7xwa, 7xxl, 7y1y, 7y1z, 7y20, 7y21, 7y75, 7y76, 7y9n, 7y9z, 7ya0, 7ya1, 7ydi, 7yeg, 7yhw, 7yj3, 7yr2, 7yr3, 7yr4, 7yv8, 7yvu, 7zdq, 7zf7, 7zr2, 7zrv, 7zsd, 7zss, 8aqs, 8aqt, 8aqu, 8aqv, 8aqw, 8bbo, 8cmb, 8cmc, 8cmd, 8cmi, 8cwk, 8czi, 8dao, 8df5, 8dlj, 8dlk, 8dlm, 8dln, 8dlp, 8dlq, 8dlu, 8dlv, 8dm5, 8dm6, 8dm7, 8dm8, 8dm9, 8dma, 8dv1, 8dv2, 8edf, 8fa1, 8fa2, 8gry, 8h06, 8h5c, 8hc6, 8hc7, 8hfx, 8hfy, 8hfz, 8hg0, 8hrk, 8hrl, 8i9b, 8i9c, 8i9d, 8i9e, 8i9f, 8i9g, 8i9h, 8if2, 8ify, 8ifz, 8iou, 8iov, 8jje, 8jyn, 8jyo, 8jyp, 8ka8, 8kc2, 8qsq, 8sph, 8spi, 8t20, 8t22, 8t25, 8taz, 8vkl, 8vkm, 8vkn, 8vko, 8vkp, 8vqr, 8wgv, 8wgw, 8wox, 8woy, 8wrh, 8wrl, 8wrm, 8wro, 8wtd, 8wtj, 8xlm, 8xln) exist and high quality models can be extracted from them but should be used with care.

High quality models are available which are predicted to form homo-trimers.

P0DTC3 · AP3A_SARS2
(275 residues)
>sp|P0DTC3|AP3A_SARS2
MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFGWLIVGVALLAVFQSAS
KIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINF
VRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPIS
EHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEP
EEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL

ORF3a protein (ORF3a)

Plays a role in viral egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels (viroporins) localized at endosomes and lysosomes, that may induce deacidification of lysosomes, allowing safe egress of virions via lysosomal trafficking (PubMed:33157038, PubMed:33422265, PubMed:34158638). Also blocks autolysosome formation by binding and sequestering the host component VPS39 for homotypic fusion and protein sorting (HOPS) on late endosomes (PubMed:33422265). This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265). Induces host RETREG1/FAM134B-dependent reticulophagy by interacting with host HMGB1 and enhancing the association between HMGB1 and host BECN1 (PubMed:35239449). This induces endoplasmic reticulum stress and inflammatory responses and facilitates viral infection (PubMed:35239449).

Experimental structures (PDB: 6xdc, 7luz, 8eqj, 8eqt) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7kjr, 8equ, 8hqt, 8t5p, 8t5q) exist and high quality models can be extracted from them but should be used with care.

High quality models are available which are predicted to form homo-dimers.

>sp|P0DTF1|ORF3B_SARS2
MMPTIFFAGILIVTTIVYLTIV

Putative ORF3b protein (ORF3b)

Acts as an interferon antagonist when expressed ex vivo.

Sequence is too short for modelling.

>sp|P0DTG1|ORF3C_SARS2
MLLLQILFALLQRYRYKPHSLSDGLLLALHFLLFFRALPKS

ORF3c protein (ORF3c)

May play a role in host modulation.

See here for template search results.

>sp|P0DTG0|ORF3D_SARS2
MAYCWRCTSCCFSERFQNHNPQKEMATSTLQGCSLCLQLAVVVCNSLLTPFARCCWP

Putative ORF3d protein

Only remote homologues were identified as potential template structures, no models have been built.

See here for template search results.

>sp|P0DTC4|VEMP_SARS2
MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYS
RVKNLNSSRVPDLLV

Envelope small membrane protein (E)

Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in the induction of apoptosis (By similarity). Regulates the localization of S protein at cis-Golgi, the place of virus budding (PubMed:33229438). May act by slowing down the cell secretory pathway (PubMed:33229438). May interfere with tight-junction stability by interacting with host MPP5. This would result in disruption of epithelial barriers, thereby amplifying inflammatory processes (PubMed:32891874).

Partial coverage by experimental structures (PDB: 7k3g, 8suz, 8u1t) is available. Partial coverage by experimental structures of hetero-oligomeric complexes exist (PDB: 7m4r, 7ntk, 7qcr, 7qcs, 7qct, 7tuq, 7tv0) and high quality models can be extracted from them but should be used with care.

Model quality estimates are low - use with care.

P0DTC5 · VME1_SARS2
(222 residues)
>sp|P0DTC5|VME1_SARS2
MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPV
TLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL
NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYK
LGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQ

Membrane protein (M)

Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins (By similarity). Regulates the localization of S protein at cis-Golgi, the place of virus budding (PubMed:33229438). May act by binding cytoplasmic c-terminus of S (PubMed:33229438).

Experimental structures (PDB: 7vgr, 7vgs, 8ctk) are available. Partial coverage by an experimental hetero-oligomeric complex (PDB: 8cme) is available and a high quality model can be extracted but should be used with care.

Only remote homologues were identified as potential template structures, no models have been built.

See here for template search results.

P0DTC6 · NS6_SARS2
(61 residues)
>sp|P0DTC6|NS6_SARS2
MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEI
D

ORF6 protein (ORF6)

Disrupts bidirectional nucleocytoplasmic transport by interacting with the host RAE1-NUP98 complex (PubMed:33360543, PubMed:33849972). Disrupts cell nuclear import complex formation by tethering karyopherin alpha 2 and karyopherin beta 1 to the membrane (PubMed:32979938). Retention of import factors at the ER/Golgi membrane leads to a loss of transport into the nucleus (By similarity). Prevents STAT1 nuclear translocation in response to interferon signaling, thus blocking the expression of interferon stimulated genes (ISGs) that display multiple antiviral activities (PubMed:33097660). Suppresses IFN-beta production possibly by blocking IRF3 nuclear translocation (PubMed:32979938). Might induce accumulation of host HNRNPA1 (PubMed:33360543) May play a role in viral double membrane vesicles networks to enhance viral replication.

Experimental structures of hetero-oligomeric complexes (PDB: 7f60, 7vph) exist and high quality models can be extracted from them but should be used with care.

Only remote homologues were identified as potential template structures, no models have been built.

See here for template search results.

P0DTC7 · NS7A_SARS2
(121 residues)
>sp|P0DTC7|NS7A_SARS2
MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFS
TQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKT
E

ORF7a protein (ORF7a)

Plays a role as antagonist of host tetherin (BST2), disrupting its antiviral effect (PubMed:33930332). Acts by binding to BST2 and sequestering it to perinuclear region, thereby preventing its antiviral function at cell membrane (PubMed:33930332). May specifically downregulate MHC-I allele HLA-A*02:01 (HLA-A2)(PubMed:36574644).

Partial coverage by experimental structures (PDB: 6w37, 7ci3) is available. Partial coverage by experimental structures of hetero-oligomeric complexes exist (PDB: 8ens, 8enw) and high quality models can be extracted from them but should be used with care.

High quality models are available.

>sp|P0DTD8|NS7B_SARS2
MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA

ORF7b protein (ORF7b)

Only remote homologues were identified as potential template structures, no models have been built.

See here for template search results.

P0DTC8 · NS8_SARS2
(121 residues)
>sp|P0DTC8|NS8_SARS2
MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIEL
CVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDF
I

ORF8 protein (ORF8)

Plays a role in modulating the host immune response (PubMed:31986261, PubMed:35343786, PubMed:36689483). May act as a secreted virokine by mimicking interleukin-17A (IL17A), and thereby binding to the IL17RA receptor, leading to activation of the IL17 pathway and increased secretion of pro-inflammatory factors (PubMed:35343786, PubMed:36689483). Contributes to the cytokine storm during SARS-CoV-2 infection when secreted by unconventional pathway (PubMed:33723527, PubMed:36689483). May act by down-regulating major histocompability complex class I (MHC-I) at cell surface (PubMed:34021074, PubMed:35157849). May inhibit expression of some members of the IFN-stimulated gene (ISG) family including hosts IGF2BP1/ZBP1, MX1 and MX2, and DHX58 (PubMed:34177923).

Experimental structures (PDB: 7f5f, 7jtl, 7jx6, 7mx9) are available. An experimental hetero-oligomeric complex (PDB: 7xmn) exists and a high quality model can be extracted but should be used with care.

High quality models are available which are predicted to form homo-dimers.

P0DTC9 · NCAP_SARS2
(419 residues)
>sp|P0DTC9|NCAP_SARS2
MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHG
KEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAG
LPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGS
QASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQ
QQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKH
WPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY
KTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA

Nucleoprotein (N)

Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M (PubMed:33264373). Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication. Attenuates the stress granules formation by reducing host G3BP1 access to host mRNAs under stress conditions (PubMed:34901782, PubMed:36534661) May block host chemokine function in vivo, facilitating viral replication and transmission (PubMed:35921414). Acts by being secreted into the extracellular space where it competes to host chemokines for binding to host glycosaminoglycans (GAG) (PubMed:35921414) May induce inflammasome responses in cultured cells and mice. Acts by interacting with host NLRP3 to facilitate inflammasome assembly, which induces cytokine release that may play a role in COVID lung injury.

Experimental structures (PDB: 6m3m, 6vyo, 6wji, 6wkp, 6wzo, 6wzq, 6yi3, 6yun, 6zco, 7acs, 7act, 7c22, 7cdz, 7ce0, 7cr5, 7de1, 7f2b, 7f2e, 7ltu, 7lux, 7lv2, 7n0i, 7n0r, 7n3c, 7n3d, 7o05, 7o35, 7o36, 7r98, 7sd4, 7str, 7sts, 7sue, 7uxx, 7uxz, 7vbd, 7vbe, 7vbf, 7vnu, 7xwx, 7xwz, 7xx1, 7xxk, 7ylb, 7yld, 8fd5, 8iqj, 8iv3, 8j6x, 8x1h) are available. Partial coverage by experimental structures of hetero-oligomeric complexes exist (PDB: 7kgo, 7kgp, 7kgq, 7kgr, 7kgs, 7kgt, 7lg0, 7lgd, 7pku, 7qik, 7qip, 7suo, 7wzo, 7zit, 8dnt, 8th1, 8th5) and high quality models can be extracted from them but should be used with care.

High quality models are available.

>sp|P0DTD2|ORF9B_SARS2
MDPKISEMHPALRLVDPQIQLAVTRMENAVGRDQNNVGPKVYPIILRLGSPLSLNMARKT
LNSLEDKAFQLTPIAVQMTKLATTEELPDEFVVVTVK

ORF9b protein (ORF9b)

Plays a role in inhibiting the host innate immune response by targeting the mitochondrial-associated innate immune response. Acts by binding to host TOMM70, inhibiting its binding to HSP90AB1 thereby disrupting the interferon activation pathway.

Experimental structures (PDB: 6z4u, 7ye7, 7ye8) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7dhg, 7kdt) exist and high quality models can be extracted from them but should be used with care.

High quality models are available which are predicted to form homo-dimers.

>sp|P0DTD3|ORF9C_SARS2
MLQSCYNFLKEQHCQKASTQKGAEAAVKPLLVPHHVVATVQEIQLQAAVGELLLLEWLAM
AVMLLLLCCCLTD

Putative ORF9c protein (ORF9c)

May induce apoptosis in cardiomyocytes when overexpressed ex-vivo.

Partial coverage by an experimental hetero-oligomeric complex (PDB: 7mb6) is available and a high quality model can be extracted but should be used with care.

Only remote homologues were identified as potential template structures, no models have been built.

See here for template search results.

>sp|A0A663DJA2|ORF10_SARS2
MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT

Putative ORF10 protein

Partial coverage by an experimental hetero-oligomeric complex (PDB: 7yc2) is available and a high quality model can be extracted but should be used with care.

No homologues were identified as potential template structures for modelling.

See here for template search results.

Hetero-Oligomeric Complexes

Show sequences
UniProtKB AC · Name
Description & Available Models
>sp|P0DTD1|R1AB_SARS2|3860-3942
SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLL
SMQGAVDINKLCEEMLDNRATLQ
>sp|P0DTD1|R1AB_SARS2|3943-4140
AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLE
KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNII
PLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNL
AWPLIVTALRANSAVKLQ

nsp7 / nsp8 hetero-oligomeric complex

Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.

Experimental structures (PDB: 6m5i, 6wiq, 6wqd, 6wtc, 6xip, 6yhu, 7dcd, 7jlt) are available.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|3860-3942
SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLL
SMQGAVDINKLCEEMLDNRATLQ
>sp|P0DTD1|R1AB_SARS2|3943-4140
AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLE
KMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNII
PLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNL
AWPLIVTALRANSAVKLQ
>sp|P0DTD1|R1AB_SARS2|4393-5324
SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKD
EDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLT
KYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYANLGE
RVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL
LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVN
CLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVN
LHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFY
DFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF
DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTIT
QMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHN
MLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECA
QVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV
RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIK
NFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGA
GCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHML
DMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ

nsp7 / nsp8 / Pol hetero-oligomeric complex

Experimental evidence for SARS-CoV that nsp7 and nsp8 activate and confer processivity to the RNA-synthesizing activity of Pol (Subissi et al., 2014 and Kirchdoerfer and Ward, 2019).

Experimental structures (PDB: 6m71, 6xqb, 6yyt, 7aap, 7b3b, 7b3c, 7b3d, 7btf, 7bv1, 7bv2, 7bw4, 7bzf, 7c2k, 7ctt, 7d4f, 7dfg, 7dfh, 7doi, 7dok, 7dte, 7krp, 7l1f, 7oyg, 7ozu, 7ozv, 7uo4, 7uo7, 7uo9, 7uob, 7uoe, 8gy6) are available.

High quality models are available

>sp|P0DTD1|R1AB_SARS2|4254-4392
AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPE
ANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVC
GMWKGYGCSCDQLREPMLQ
>sp|P0DTD1|R1AB_SARS2|5926-6452
AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGF
KMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAV
PTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDR
VVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPF
MIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIG
DELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKA
YKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLY
VNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLG
GAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

nsp10 / nsp14 hetero-oligomeric complex

Nsp10 plays a pivotal role in viral transcription by stimulating nsp14 3'-5' exoribonuclease activity.

Experimental structures (PDB: 7diy, 7mc5, 7mc6, 7n0b, 7n0c, 7n0d) are available.

High quality models are available.

>sp|P0DTD1|R1AB_SARS2|4254-4392
AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPE
ANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVC
GMWKGYGCSCDQLREPMLQ
>sp|P0DTD1|R1AB_SARS2|6799-7096
SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLA
VPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHT
ANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADL
YKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLS
SYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

nsp10 / nsp16 hetero-oligomeric complex

Nsp10 plays a pivotal role in viral transcription by stimulating nsp16 2'-O-ribose methyltransferase activity.

Experimental structures (PDB: 6w4h, 6w61, 6w75, 6wjt, 6wkq, 6wks, 6wq3, 6wrz, 6wvn, 6xkm, 6yz1, 7bq7, 7c2i, 7c2j, 7jhe, 7jib, 7jpe, 7jyy, 7jz0, 7koa, 7l6r, 7l6t, 7lw3, 7lw4, 7r1t, 7r1u, 7ult, 8a23, 8bsd, 8bzv, 8c5m, 8f4s, 8f4y, 8osx, 8ot0, 8oto, 8otr, 8ov1, 8ov2, 8ov3, 8ov4, 8rv4, 8rv5, 8rv6, 8rv7, 8rv8, 8rv9, 8rva, 8rvb, 8rzc, 8rzd, 8rze, 8s8w, 8s8x, 8tyj, 9emj, 9eml, 9emv, 9eun) are available.

High quality models are available.

P0DTC2 · SPIKE_SARS2
(1273 residues)
>sp|P0DTC2|SPIKE_SARS2
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
SEPVLKGVKLHYT
Q9BYF1 · ACE2_HUMAN
(805 residues)
>sp|Q9BYF1|ACE2_HUMAN
MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQ
NMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTIL
NTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLY
EEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHL
HAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILM
CTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKS
IGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEM
KREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLH
KCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
NSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKN
QMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDN
SLEFLGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKKNKARSGENP
YASIDISKGENNPGFQNTDDVQTSF

Spike glycoprotein / ACE2_HUMAN hetero-oligomeric complex

Spike protein S1 binds to human ACE2, initiating the infection.

Experimental structures (PDB: 6lzg, 6m0j, 6vw1, 7a91, 7a92, 7a94, 7a95, 7a96, 7a97, 7a98, 7bh9, 7ct5, 7df4, 7dmu, 7dqa, 7dx4, 7dx5, 7dx6, 7dx7, 7dx8, 7dx9, 7edj, 7efp, 7efr, 7ekc, 7eke, 7ekf, 7ekg, 7ekh, 7fdg, 7fdh, 7fdi, 7fem, 7kj2, 7kj3, 7kj4, 7kmb, 7kms, 7kmz, 7knb, 7kne, 7knh, 7kni, 7l0n, 7l7f, 7lo4, 7mjm, 7mjn, 7nxc, 7p19, 7r0z, 7r10, 7r11, 7r12, 7r1a, 7rpv, 7sn0, 7sxx, 7sxy, 7sxz, 7sy0, 7sy1, 7sy2, 7sy3, 7sy4, 7sy5, 7sy6, 7sy7, 7sy8, 7t9k, 7t9l, 7tew, 7tex, 7tez, 7tf0, 7tn0, 7u0n, 7ufk, 7ufl, 7v7z, 7v80, 7v81, 7v82, 7v83, 7v84, 7v85, 7v86, 7v87, 7v88, 7v89, 7v8a, 7v8b, 7vx4, 7vx5, 7vx9, 7vxa, 7vxb, 7vxc, 7vxd, 7vxf, 7vxk, 7vxm, 7w99, 7w9b, 7w9c, 7wbl, 7wbp, 7wbq, 7wgb, 7wgc, 7whh, 7wk4, 7wk5, 7wk6, 7wnm, 7wpa, 7wpb, 7wpc, 7ws8, 7ws9, 7wsa, 7wvp, 7wvq, 7xaz, 7xb0, 7xb1, 7xch, 7xci, 7xcp, 7xid, 7xo7, 7xo8, 7xo9, 7xwa, 7y1y, 7y1z, 7y20, 7y21, 7y9z, 7ya0, 7ya1, 7ydi, 7yeg, 7yhw, 7yj3, 7yr2, 7yr3, 7yr4, 7zdq, 7zf7, 8aqs, 8df5, 8dlj, 8dlk, 8dlm, 8dln, 8dlp, 8dlq, 8dlu, 8dlv, 8dm5, 8dm6, 8dv1, 8dv2, 8h06, 8h5c, 8hrk, 8hrl, 8i9b, 8i9c, 8i9d, 8i9e, 8i9f, 8i9g, 8i9h, 8if2, 8iou, 8iov, 8jje, 8jyn, 8jyo, 8jyp, 8qsq, 8sph, 8spi, 8vko, 8vkp, 8vqr, 8wgv, 8wgw, 8wrh, 8wrl, 8wrm, 8wro, 8wtd, 8wtj, 8xlm, 8xln) are available.

High quality models are available.

Structural Analysis of Mutations

We downloaded SARS-CoV-2 mutation data from GISAID (July 3, 2021) and computed the frequencies of every observed mutation. We summarized the number of different mutations observed at each residue position and summed the frequencies for each residue. For insertions and deletions the frequencies were assigned to the previous residue, except for N-terminal insertions which were assigned to the first residue of the protein.

We performed proximity searches within an 8A radius, and summed both frequencies and number of mutations (excluding the residue itself). To normalize the mutations we first computed the residue-level average of frequencies and number of mutations for each UniProt protein. We then subtracted this baseline value from each residue in the proximity that was mapped to a SARS-CoV-2 protein by SIFTS.

Residue-level analysisProximity (8A)Proximity (8A, normalized)
Number of mutationView resultsView resultsView results
Number of mutation (in binding sites)View resultsView resultsView results
Mutation frequencyView resultsView resultsView results
Mutation frequency (in binding sites)View resultsView resultsView results

Click on a project to list its content on the SWISS-MODEL Repository.
We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based. You can download the full list of sequence IDs, submission date and location used in the analysis here.
If you use this data in a publication, please cite: Elbe S., and Buckland-Merrett G. (2017) "Data, disease and diplomacy: GISAID’s innovative contribution to global health." Global Challenges 1: 33-46
Part of the analysis was performed by collaborators at the Computational Biology group of BSC-CNS within the EXSCALATE4CoV project.