Replicase polyprotein 1ab

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

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

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). 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) 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.

Non-structural protein 2 (nsp2)

May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.

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

High quality models are available.

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 (By similarity). 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 DDX58 (RIG-I) (PubMed:33727702). Can play a role in host ADP-ribosylation by binding ADP-ribose (PubMed:32578982).

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, 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, 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, 7pku, 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) is available. Partial coverage by experimental structures of hetero-oligomeric complexes exist (PDB: 6xa9, 6xaa, 6yva, 7rbr, 7rbs, 7uv5) 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.

Non-structural protein 4 (nsp4)

Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.

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

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). Also able to bind an ADP-ribose-1''-phosphate (ADRP) (By similarity) (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, 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, 7fay, 7faz, 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, 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, 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, 7qbb, 7ql8, 7qt5, 7qt6, 7qt7, 7qt8, 7r7h, 7rbz, 7rc0, 7rfr, 7rfs, 7rfu, 7rfw, 7rls, 7rm2, 7rmb, 7rme, 7rmt, 7rmz, 7rn0, 7rn1, 7rn4, 7rnh, 7rnk, 7rnw, 7s3k, 7s3s, 7s4b, 7s82, 7si9, 7t42, 7t43, 7t44, 7t45, 7t46, 7t48, 7t49, 7t4a, 7t4b, 7tdu, 7te0, 7teh, 7tfr, 7tgr, 7tia, 7tiu, 7tiv, 7tiw, 7tix, 7tiy, 7tiz, 7tj0, 7tll, 7tob, 7tq5, 7tq6, 7tvx, 7u28, 7u29, 7vah, 7vfa, 7vfb, 7vh8, 7vic, 7vjw, 7vjx, 7vjy, 7vjz, 7vk0, 7vk1, 7vk2, 7vk3, 7vk4, 7vk5, 7vk6, 7vk7, 7vk8, 7vlp, 7vlq, 7vth, 7vu6, 7vvt, 7wo1, 7wo3, 7wof, 7woh, 7z0p) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7dvp, 7dvw, 7dvx, 7dvy, 7dw0, 7dw6, 7lmc, 7mgr, 7mgs, 7n6n, 7n89) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

Non-structural protein 6 (nsp6)

Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic (By similarity). Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes (By similarity). 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.

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, 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm) exist and high quality models can be extracted from them but should be used with care.

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, 7oyg, 7ozu, 7ozv, 7rdx, 7rdy, 7rdz, 7re0, 7re1, 7re2, 7re3, 7thm) exist and high quality models can be extracted from them but should be used with care.

Non-structural protein 9 (nsp9)

May participate in viral replication by acting as a ssRNA-binding protein (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).

Experimental structures (PDB: 6w4b, 6w9q, 6wc1, 6wxd, 7bwq, 7kri, 7n3k) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7cyq, 7egq, 7eiz, 7thm) 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.

Non-structural protein 10 (nsp10)

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

Experimental structures (PDB: 6zct, 6zpe, 7orr, 7oru, 7orv, 7orw) 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, 7mc5, 7mc6, 7n0b, 7n0c, 7n0d, 7ult) 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.

RNA-directed RNA polymerase nsp12 (Pol)

Responsible for replication and transcription of the viral RNA genome.

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) exist and high quality models can be extracted from them but should be used with care.

Helicase nsp13 (Hel)

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) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

Proofreading exoribonuclease nsp14 (ExoN)

Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Acts as a proofreading exoribonuclease for RNA replication, thereby lowering The sensitivity of the virus to RNA mutagens.

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) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7diy, 7egq, 7eiz, 7mc5, 7mc6, 7n0b, 7n0c, 7n0d) 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.

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).

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) are available.

High quality models are available.

2'-O-methyltransferase nsp16

Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs (By similarity). N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system (By similarity). 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, 7ult) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

Spike glycoprotein (S glycoprotein)

Spike glycoprotein (14-1273): May down-regulate host tetherin (BST2) by lysosomal degradation, thereby counteracting its antiviral activity. Spike protein S1 (14-685): Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection. Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32221306, PubMed:32075877, PubMed:32155444). Binding to host NRP1 and NRP2 via C-terminal polybasic sequence enhances virion entry into host cell (PubMed:33082294, PubMed:33082293). This interaction may explain virus tropism of human olfactory epithelium cells, which express high level of NRP1 and NRP2 but low level of ACE2 (PubMed:33082293). The stalk domain of S contains three hinges, giving the head unexpected orientational freedom (PubMed:32817270). Uses human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Can be alternatively processed by host furin (PubMed:32362314). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membrane fusion within endosomes. Spike protein S2 (686-1273): Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. 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 viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Spike protein S2' (816-1273): Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.

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, 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, 7ey0, 7ey5, 7ezv, 7f46, 7f62, 7f63, 7f7e, 7fae, 7faf, 7fcd, 7fce, 7fet, 7fg2, 7fg3, 7fg7, 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, 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, 7ny5, 7oan, 7oao, 7oap, 7oaq, 7oau, 7oay, 7od3, 7odl, 7olz, 7or9, 7ora, 7orb, 7owx, 7p40, 7p77, 7p78, 7p79, 7p7a, 7p7b, 7phg, 7pqy, 7pqz, 7pr0, 7pry, 7prz, 7ps0, 7ps1, 7ps2, 7ps4, 7ps5, 7ps6, 7ps7, 7q0a, 7q0g, 7q0h, 7q0i, 7q1z, 7q6e, 7q9f, 7q9g, 7q9i, 7q9j, 7q9k, 7q9m, 7q9p, 7qnw, 7qnx, 7qny, 7qo7, 7qo9, 7r13, 7r14, 7r15, 7r16, 7r17, 7r18, 7r19, 7r1b, 7r40, 7r6w, 7r6x, 7r7n, 7r8l, 7r8m, 7r8n, 7r8o, 7r95, 7ra8, 7ral, 7raq, 7rbv, 7rby, 7rku, 7rkv, 7rnj, 7rq6, 7rr0, 7rw2, 7s0b, 7s0c, 7s0d, 7s0e, 7s3n, 7s4s, 7s5p, 7s5q, 7s5r, 7s6i, 7s6j, 7s6k, 7s6l, 7sbk, 7sbl, 7sbo, 7sbp, 7sbq, 7sbr, 7sbs, 7sbt, 7sbu, 7sc1, 7sd5, 7si2, 7sjs, 7sn2, 7sn3, 7so9, 7soa, 7sob, 7soc, 7sod, 7soe, 7sof, 7spo, 7spp, 7swn, 7swo, 7swp, 7sxr, 7sxs, 7sxt, 7sxu, 7sxv, 7sxw, 7t01, 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, 7tpl, 7tpr, 7u0d, 7u2d, 7u2e, 7uap, 7uaq, 7uar, 7ub0, 7ub5, 7ub6, 7urq, 7urs, 7v26, 7v2a, 7v76, 7v77, 7v78, 7v79, 7v7a, 7v7d, 7v7e, 7v7f, 7v7g, 7v7h, 7v7i, 7v7j, 7v7n, 7v7o, 7v7p, 7v7q, 7v7r, 7v7s, 7v7t, 7v7u, 7v7v, 7v8c, 7vmu, 7vnb, 7vnc, 7vnd, 7vne, 7vx1, 7vxe, 7vxi, 7vyr, 7w92, 7w94, 7w9e, 7w9f, 7wcr, 7wcz, 7wd0, 7wd7, 7wd8, 7wd9, 7wdf, 7we7, 7we8, 7we9, 7wea, 7web, 7wec, 7wed, 7wee, 7wef, 7wev, 7whi, 7whj, 7whk, 7wk2, 7wk3, 7wk8, 7wk9, 7wka, 7wlc, 7wp9, 7wpd, 7wpe, 7wpf, 7wph, 7wrv, 7wue, 7wuh, 7x7d, 7x7e, 7x7n, 7x9e, 7z0x, 7z0y, 7z1a, 7z1b, 7z1c, 7z1d, 7z1e, 7z3z) 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, 7e3j, 7e8f, 7edj, 7efp, 7efr, 7ek6, 7ekc, 7eke, 7ekf, 7ekg, 7ekh, 7ey4, 7eya, 7fdg, 7fdh, 7fdi, 7fdk, 7fem, 7kj2, 7kj3, 7kj4, 7kmb, 7kms, 7kmz, 7knb, 7kne, 7knh, 7kni, 7l0n, 7l7f, 7lo4, 7mjm, 7mjn, 7nxc, 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, 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, 7wk4, 7wk5, 7wk6, 7wpa, 7wpb, 7wpc, 7wvp, 7wvq) 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.

ORF3a protein (ORF3a)

Plays a role in viral egress via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Forms homotetrameric ion channels (viroporin) localized at endosomes and lysosomes, that may induce deacidification of lysosomes, allowing safe egress of virions via lysosomal trafficking (PubMed:33157038, PubMed:33422265). Also blocks autolysosomes formation by binding and sequestering the host component VPS39 for homotypic fusion and protein sorting (HOPS) on late endosomes. This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress (PubMed:33422265).

Experimental structures (PDB: 6xdc, 7luz) are available. An experimental hetero-oligomeric complex (PDB: 7kjr) 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.

Putative ORF3b protein (ORF3b)

Acts as an interferon antagonist when expressed ex vivo.

Sequence is too short for modelling.

ORF3c protein (ORF3c)

May play a role in host modulation.

See here for template search results.

Putative ORF3d protein

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

See here for template search results.

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

Model quality estimates are low - use with care.

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).

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

See here for template search results.

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).

Partial coverage by an experimental hetero-oligomeric complex (PDB: 7vph) 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.

ORF7a protein (ORF7a)

Plays a role as antagonist of host tetherin (BST2), disrupting its antiviral effect. Acts by binding to BST2 and sequestering it to perinuclear region, thereby preventing its antiviral function at cell membrane.

Partial coverage by experimental structures (PDB: 6w37, 7ci3) is available.

High quality models are available.

ORF7b protein (ORF7b)

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

See here for template search results.

ORF8 protein (ORF8)

Plays a role in modulating host immune response (PubMed:31986261). May act by down-regulating major histocompability complex class I (MHC-I) (PubMed:34021074). May inhibit expression of some members of the IFN-stimulated gene (ISG) family including hosts IGF2BP1/ZBP1, MX1 and MX2, and DHX58 (PubMed:34177923). Binds to IL17RA receptor, leading to IL17 pathway activation and an increased secretion of pro-inflammatory factors. Contributes to cytokine storm during COVID-19 infection (PubMed:33723527).

Experimental structures (PDB: 7f5f, 7jtl, 7jx6) are available.

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

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. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication (By similarity) 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.

Partial coverage by 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, 7pku, 7r98, 7vnu) is available. Partial coverage by experimental structures of hetero-oligomeric complexes exist (PDB: 7kgo, 7kgp, 7kgq, 7kgr, 7kgs, 7kgt, 7lg0, 7lgd, 7qik, 7qip, 7suo) and high quality models can be extracted from them but should be used with care.

High quality models are available.

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, disrupting its role in the interferon activation pathway.

An experimental structure (PDB: 6z4u) is 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.

Putative ORF9c protein (ORF9c)

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

See here for template search results.

ORF10 protein

No homologues were identified as potential template structures for modelling.

See here for template search results.