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.

Host translation inhibitor nsp1

Inhibits host translation by associating with the open head conformation of the 40S subunit (PubMed:32680882, PubMed:32908316, PubMed:33080218, PubMed:33479166). The C-terminus binds to and obstructs ribosomal mRNA entry tunnel (PubMed:32680882, PubMed:32908316, PubMed:33080218, PubMed:33479166). Thereby inhibits antiviral response triggered by innate immunity or interferons (PubMed:32680882, PubMed:32979938, PubMed:33080218). 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, 8rf2, 8rf3, 8rf4, 8rf5, 8rf6, 8rf8, 8rfc, 8rfd, 8rff) 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)

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.

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, 8jux, 8sh6, 8sh8, 8tv6, 8tv7, 8ufm, 8uob, 8uuf, 8uug, 8uuh, 8uuu, 8uuv, 8uuw, 8uuy, 8uvm, 8vec, 8xab, 8yx2, 8yx3, 8yx4, 8yx5, 9azx, 9brv, 9brw, 9brx, 9csy) is available. Experimental structures of hetero-oligomeric complexes (PDB: 6xa9, 6xaa, 6yva, 7pku, 7rbr, 7rbs, 7uv5, 7wzo, 8cx9, 8yax, 8yb5, 8yb7) exist 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)

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).

Experimental structures of hetero-oligomeric complexes (PDB: 7lmc, 7mb4, 8yax, 8yb5, 8yb7) exist and high quality models can be extracted from them but should be used with care.

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). 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, 7shb, 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, 8aj1, 8b0s, 8b0t, 8b2t, 8bfo, 8bfq, 8bga, 8bgd, 8bs1, 8bs2, 8c9l, 8c9o, 8c9p, 8c9q, 8c9u, 8ca6, 8ca8, 8cac, 8caj, 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, 8k67, 8k68, 8k6a, 8k6b, 8k6c, 8k6d, 8okb, 8okc, 8okk, 8okl, 8okm, 8okn, 8p54, 8p55, 8p56, 8p57, 8p58, 8p5a, 8p5b, 8p5c, 8p86, 8p87, 8ph4, 8r0v, 8r11, 8r12, 8r14, 8r16, 8r19, 8r1q, 8r24, 8r26, 8rjz, 8s9z, 8sg6, 8sk4, 8skh, 8spj, 8sty, 8stz, 8sxo, 8sxr, 8t7y, 8tbe, 8tpb, 8tpc, 8tpd, 8tpg, 8tph, 8tpi, 8tqh, 8tqj, 8tql, 8tqt, 8tqu, 8ty3, 8ty4, 8ty5, 8tyk, 8u25, 8u3o, 8u4y, 8u9h, 8u9k, 8u9m, 8u9n, 8u9t, 8u9u, 8u9v, 8u9w, 8uab, 8uh5, 8uh8, 8uh9, 8uho, 8uia, 8uif, 8ups, 8upv, 8upw, 8ur9, 8ute, 8v4u, 8v7t, 8v7w, 8v8e, 8v8g, 8vd7, 8vdj, 8vqx, 8vsg, 8w1t, 8w1u, 8ws3, 8wsh, 8wsi, 8wsk, 8wti, 8wur, 8wzp, 8wzq, 8ya5, 8ykj, 8ykm, 8ykn, 8yko, 8ykp, 8ykq, 8yls, 8yrh, 8ysa, 9arq, 9ars, 9art, 9asv, 9asw, 9asy, 9asz, 9at0, 9at1, 9at3, 9at4, 9at5, 9at6, 9at7, 9auj, 9auk, 9aul, 9aum, 9aun, 9auo, 9avq, 9bpf, 9c80, 9c8q, 9cmj, 9cmn, 9cms, 9cmu, 9eo6, 9eor, 9eox, 9epl, 9epm, 9fq9, 9fqa, 9fx6, 9fx7, 9gij, 9gil, 9glv, 9hak, 9hbq, 9hc1, 9hd8, 9hdc, 9hdj, 9hdn, 9hjh, 9ik2) 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, 8ddl, 8eir, 8h7k, 8wsj, 9dw6) 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 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.

Non-structural protein 7 (nsp7)

Plays a role in viral RNA synthesis (PubMed:32277040, PubMed:32358203, 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.

Non-structural protein 8 (nsp8)

Plays a role in viral RNA synthesis (PubMed:32277040, PubMed:32358203, 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, 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.

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, 8wke) 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.

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, 9fw2, 9fz4, 9fzk, 9gny, 9grp, 9grq, 9gs4, 9gtf, 9gud, 9gue, 9guf, 9guy, 9gwo) 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)

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, 8xko) exist and high quality models can be extracted from them but should be used with care.

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, 8rne, 8rnf) exist and high quality models can be extracted from them but should be used with care.

High quality models are available.

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, 9feh) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7diy, 7egq, 7eiz, 7mc5, 7mc6, 7n0b, 7n0c, 7n0d, 8cmg, 9fw2, 9fz4, 9fzk) 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). 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, 9bih) 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 (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, 9gny, 9grp, 9grq, 9gs4, 9gtf, 9gud, 9gue, 9guf, 9guy, 9gwo) 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 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:32155444, PubMed:33607086). 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:32075877, PubMed:32221306). 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, 6lxt, 6m1v, 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, 7cot, 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, 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, 8c0y, 8c1v, 8c2r, 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, 8hlc, 8hld, 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, 8jap, 8jin, 8jio, 8jmm, 8jva, 8jyk, 8jym, 8jys, 8k18, 8k19, 8k3k, 8k45, 8k46, 8k47, 8k5g, 8k5h, 8k9b, 8k9j, 8k9m, 8kdr, 8keh, 8kej, 8keo, 8kep, 8keq, 8ker, 8khc, 8khd, 8owt, 8owv, 8oww, 8oyt, 8oyu, 8p5m, 8p99, 8p9y, 8pq2, 8psd, 8q5y, 8q7s, 8q93, 8q94, 8q95, 8qpr, 8qq0, 8qrf, 8qrg, 8qtd, 8qzr, 8r1c, 8r80, 8r8k, 8rby, 8rj7, 8rrn, 8sdf, 8sdg, 8sdh, 8sgu, 8siq, 8sir, 8sis, 8sit, 8sk5, 8smi, 8smt, 8suo, 8swh, 8t21, 8thf, 8tm1, 8tma, 8tmy, 8tyl, 8tyo, 8u1g, 8u28, 8ug9, 8uir, 8uk1, 8ukd, 8ukf, 8upx, 8usz, 8uul, 8uum, 8uun, 8uuo, 8v0l, 8v0m, 8v0n, 8v0o, 8v0p, 8v0q, 8v0r, 8v0s, 8v0t, 8v0u, 8v0v, 8v0w, 8v0x, 8v4f, 8v5v, 8vao, 8vcr, 8vif, 8vke, 8vkk, 8vye, 8vyf, 8vyg, 8w4f, 8wfh, 8wfm, 8whv, 8whw, 8wlo, 8wlr, 8wmd, 8wmf, 8wpw, 8wpy, 8wxl, 8wyj, 8wzi, 8x0x, 8x0y, 8x4h, 8x4z, 8x50, 8x55, 8x56, 8x5q, 8x5r, 8xbf, 8xe9, 8xea, 8xef, 8xi6, 8xk2, 8xki, 8xlv, 8xm5, 8xmg, 8xmt, 8xrq, 8xse, 8xsi, 8xsl, 8xur, 8xus, 8xut, 8xuu, 8xux, 8y0y, 8y4a, 8y4c, 8y5j, 8yro, 8yrp, 8yww, 8ywx, 8yz5, 8yz6, 8zby, 8zbz, 8zc0, 8zc1, 8zc2, 8zc3, 8zc4, 8zc5, 8zc6, 8zer, 8zes, 8zhd, 8zhe, 8zhf, 8zhg, 8zhh, 8zhi, 8zhj, 8zhk, 8zhl, 8zhm, 8zhn, 8zho, 8zhp, 9ato, 9atp, 9au2, 9ayw, 9ayx, 9ayy, 9b82, 9c44, 9c45, 9co6, 9co7, 9co8, 9co9, 9crc, 9crd, 9cre, 9crf, 9crg, 9crh, 9cri, 9f9y, 9fgr, 9fgs, 9fgt, 9fgu, 9fjk, 9gdx, 9gdy) 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, 8qh0, 8qh1, 8qsq, 8sph, 8spi, 8t20, 8t22, 8t25, 8taz, 8uze, 8via, 8vkl, 8vkm, 8vkn, 8vko, 8vkp, 8vqr, 8wdr, 8wds, 8wdy, 8wdz, 8we0, 8we1, 8we4, 8wgv, 8wgw, 8whs, 8whu, 8whz, 8wox, 8woy, 8wp8, 8wrh, 8wrl, 8wrm, 8wro, 8wtd, 8wtj, 8wyh, 8xlm, 8xln, 8xn2, 8xn3, 8xn5, 8xnf, 8xnk, 8xsf, 8xsj, 8xuy, 8xuz, 8xv0, 8xv1, 8xvm, 8xxw, 8xyz, 8xz8, 8xz9, 8xza, 8xzd, 8y16, 8y18, 8y32, 8y6a, 8yf2, 8yft, 8zbq, 9iu1) 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 (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, 8eqj, 8eqt) are available. Experimental structures of hetero-oligomeric complexes (PDB: 7kjr, 8equ, 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.

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 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.

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, 9ctu, 9ctw) 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.

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.

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.

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 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.

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, 7luz, 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, 8r6e, 8tfd, 8x1h, 9cj6, 9evy, 9ewh, 9exb, 9ezb, 9f2g, 9f2h, 9f2i, 9f5j, 9f5l, 9f7a, 9f7c, 9f83, 9fbg) 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.

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.

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.

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.