Spike protein 3D structures

3D Structures of spike protein

Updated on 04-December-2023

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• Human virus spike protein; Domains – N terminal (NTD) 1-303; Receptor Binding Domain (RBD) 318-510; HR1 910-1054; HR2 1162-1286; transmembrane (TM) 1217-1237
  • 5wrg, 5xlr, 6acc, 6acd, 6x2b, 6xr8, 6xra, 6zb4, 6zb5, 6zge, 6zgg, 6zgh, 6zgi, 7dzw, 7fb0, 7fb1, 7fb3, 7fb4, 7m0j, 7zh1, 7zh2, 7zh5, 8d55, 8d56, 8d5a, 8fez, 8h15, 8h16, 8h3d – hscvSpi – human SARS-CoV – Cryo EM
    
  • 6crv, 6crw, 6crx, 6crz, 6cs0, 6cs1, 6x29, 6x2a, 6x2c, 6zox, 6zoy, 6zoz, 6zp0, 6zp1, 6zp2, 7bnm, 7cn9, 7kdg, 7kdh, 7kdi, 7kdj, 7kdk, 7kdl, 7ke4, 7ke6, 7ke7, 7ke8, 7ke9, 7kea, 7keb, 7kec, 7krq, 7krr, 7krs, 7lwi, 7lwj, 7lwk, 7lwl, 7lwm, 7lwn, 7lwo, 7lwp, [[[7lwq|7lwq]], 7lww, 7mjg, 7od3, 7odl, 7sxr, 7sxs, 7sxt, 7sxu, 7sxv, 7sxw, 7tp1, 7vhn, 7xtz, 7xu0, 7xu1, 7xu2, 7xu3, 7xu4, 7xu5, 7xu6, 8csa, 8h0x, 8h0y, 8h0z, 8h10, 8h11, 8h12, 8h13, 8h14, 8p99, 8p9y, 8t21 – hscvSpi (mutant) – Cryo EM
    
  • 1wnc – hscvSpi HR1 motif
    
  • 7r95 – hscvSpi HR1- NMR
    
  • 6lvn – hscvSpi HR2
    
  • 2fxp – hscvSpi HR2 motif 1140-1193 - NMR
    
  • 7owx – hscvSpi stalk 1177-1203
    
  • 2ghv – hscvSpi RBD
    
  • 7tpk – hscvSpi RBD (mutant) – Cryo EM
    
  • 5xjk – hscvSpi 758-821 - NMR
    
  • 1wyy – hscvSpi 885-1189
    
  • 1zv7, 1zv8, 1zva, 1zvb – hscvSpi 1150-1193
    
  • 8fdw, 7e9t – hscvSpi 686-1273 – Cryo EM
    
  • 7lc8 – hscvSpi TM - NMR
    
  • 7wxz, 7y9n, 7zr2 – hscvSpi HR1 + HR2
    
  • 7rzq, 7rzs, 8czi – hscvSpi HR1 + HR2 – Cryo EM
    
  • 7rzr, 7rzt, 7rzu, 7rzv, 8fa1 – hscvSpi HR1 (mutant) + HR2 – Cryo EM
    
  • 8fa2 – hscvSpi HR1 + 42G – Cryo EM
    
  • 6u7h – hcv229Spi – human coronavirus 229E – Cryo EM
    
  • 5zuv, 5zvm – hcv229Spi HR1 motif 785-873
    
  • 5yl9, 5zhy – hcv229Spi HR1+HR2 motifs
    
  • 5x58, 5x5b – Spi – human SARS coronavirus BJ01 – Cryo EM
    
  • 6vsb, 6vxx, 6vyb – hsc2Spi – human SARS coronavirus 2 – Cryo EM
    
  • 6lxt – hscSpi HR1+HR2 motifs
    
  • 5szs – hcnSpi – human coronavirus NL63 - Cryo EM
    
  • 2ieq – hcnSpi HR1+HR2 motifs
    
  • 6cv0 – Spi – infectious bronchitis coronavirus – Cryo EM
    
  • 5fyn – Spi ectodomain - puumala virus - Cryo EM
    
  • 5x59, 5x5c, 5x5f, 6q04, 6q05, 6q06, 6q07, 7yn0 – McvSpi – MERS coronavirus virus – Cryo EM
    
  • 7ymt, 7ymv, 7ymw, 7ymx, 7ymy, 7ymz – McvSpi (mutant) – Cryo EM
    
  • 5x4r, 5x4s – McvSpi NTD – Cryo EM
    
  • 5vyh – McvSpi NTD
    
  • 4zpw, 4kqz – McvSpi RBD
    
  • 4mod – McvSpi HR1+HR2 motifs
    
  • 2lcz, 2lcy - ZevSpi fusion loop 507-560 - Zaire ebolavirus - NMR
    
  • 2m5f, 2mb1 - ZevSpi fusion loop (mutant) - NMR
    
• Human virus spike protein alpha
  • 8dli – hscvSpi – Cryo EM
    
• Human virus spike protein beta
  • 7vx1, 7wev, 8dll – hscvSpi – Cryo EM
    
  • 5gnb, 5kwb – hscvSpi RBD
    
• Human virus spike protein gamma
  • 7sbp, 7sbs, 8dlo – hscvSpi – Cryo EM
    
  • 7sbt – hscvSpi (mutant) – Cryo EM
    
• Human virus spike protein delta
  • 7sbk, 7sbl, 7tey, 7w94 – hscvSpi – Cryo EM
    
  • 7sbo, 7tl1, 7tl9, 7tou, 7tov, 7tox, 7toy, 7toz, [[[7tp0|7tp0]], 7tp2, 7tp7, 7tp8, 7tp9, 7tpa, 7tpc, 7tpe, 7tpf, 7tph, 7tpl, 7vhh, 7w92 – hscvSpi (mutant) – Cryo EM
    
• Human virus spike protein epsilon
  • 8dlt – hscvSpi – Cryo EM
    
• Human virus spike protein kappa
  • 7sbq, 7sbr, 7tf2, 7tf5, 7vxe, 7vxi – hscvSpi – Cryo EM
    
  • 7tf3 – hscvSpi (mutant) – Cryo EM
    
  • 7tf1, 7tf4 – hscvSpi RBD – Cryo EM
    
• Human virus spike protein omicron
  • 7t9j, 7tge, 8dm1 – hscvSpi – Cryo EM
    
  • 7tei – hscvSpi (muant) – Cryo EM
    
  • 7tf8, 7ub0, 7ub5, 7ub6, 7x1m, 7y9s – hscvSpi (mutant) – Cryo EM
    
  • 8dm2 – hscvSpi NTD – Cryo EM
    
  • 7uad, 7xiz – hscvSpi RBD – Cryo EM
    
• South African spike protein
  • 7lyk, 7lyl, [[7lym], 7lyn, 7lyo, 7lyp, 7lyq – hscvSpi (mutant) – Cryo EM
    
  • 7fjn, 7fjo – hscvSpi (mutant) + antibody– Cryo EM
    
• UK spike protein
  • 7lws, 7lwt, 7lwu, 7lwv – hscvSpi (mutant) – Cryo EM
    
• Human virus spike protein complex with antibody
  • 6nb6, 6nb7, 7cwl, 7cwm, 7cwn, 7cwt, 7dzx, 7dzy, 7k9k, 7kxj, 7kxk, 7l3n, 7ljr, 7q0a, 7rbu, 7swn, 7wef, 7wp1, 7wp6, 7x6a, 7zjl, 8d0z, 8dtk, 8gsb, 8iv8, 8iva – hscvSpi + antibody - Cryo EM
    
  • [[7mjj], 7mjl, 8gnh] – hscvSpi (mutant) + antibody - Cryo EM
    
  • 2dd8, 2ghw, 3bgf, 6w41, 6xc2, 6xc3, 6xc4, 6xc7, 6xe1, 6xkp, 6xkq, 6zer, 7b3o, 7bwj, 7bz5, 7c01, 7cdi, 7cdj, 7ch4, 7ch5, 7chb, 7chc, 7che, 7chf, 7cho, 7chp, 7chs, 7cjf, 7d6i, 7djz, 7dk0, 7dk2, 7dpm, 7e3o, 7e5o, 7e5y, 7e7y, 7e86, 7e88, 7eam, 7ean, 7ejy, 7f6z, 7f7e, 7fcp, 7fcq, 7fjs, 7jmo, 7jmp, 7jmw, 7jx3, 7k9z, 7kmg, 7kn3, 7kn4, 7l5b, 7l7d, 7l7e, 7lm8, 7lm9, 7lop, 7lq7, 7m3i, 7m6d, 7m7w, 7mf1, 7msq, 7mzf, 7mzg, 7mzh, 7mzi, 7mzj, 7mzk, 7mzl, 7mzm, 7mzn, 7n3i, 7n4i, 7n4j, 7n4l, 7n4m, 7np1, 7nx6, 7nx8, 7nxa, 7nxb, 7or9, 7orb, 7pqy, ]]7pqz]], 7pr0, 7qez, 7qf0, 7qf1, 7r6w, 7r6x, 7r8l, 7rks, 7rku, 7s0b, 7s4s, 7s5p, 7s5q, 7s5r, 7s83, 7sbu, 7sd5, 7si2, 7t7b, 7te1, 7tp3, 7tp4, 7u2d, 7u2e, 7u8e, 7ul0, 7ul1, 7uzc, 7uzd, 7vmu, 7vn9, 7nyr, 7vzt, 7wbz, 7wn2, 7wnb, 7wqv, 7wph, 7wue, 7wvl, 7x2h, 7x7o, 7xei, 7xnf, 7xs8, 7xsa, 7xsc, 7y0c, 7y0v, 7yck, 7ycl, 7ycn, 7yh6, 7z0x, 7z0y, 8be1, 8cwi, 8cwk, 8dcc, 8dnn, 8dpz, 8dw9, 8dwa, 8dxt, 8dxu, 8edf, 8el2, 8eoo, 8f0i, 8gb6, 8hes, 8hn6, 8hn7, 8gb5, 8gb7, 8gb8, 8gf2, 8gx9, 8smt – hscvSpi RBD + antibody
    
  • 6xdg, 6zdg, 6zfo, 7cah, 7cwo, 7e23, 7e39, 7e3b, 7e3c, 7k9i, 7m42, 7mkm, 7mlz, 7rr0, 7swo, 7swp, 7t01, 7tbf, 7tc9, 7the, 7v27, 7whz, 7wo7, 7wp1, 7wp2, 7wp8, 7wr8, 7wr9, 7wrj, 7wsc, 7x7t, 7x7v, 7xxl, 7y7k, 7yr0, 8a96, 8dw2, 8gjn, 8h7l, 8hed, 8idn, 8iv4, 8iv5, 8ix3, 8pq2 – hscvSpi RBD + antibody – Cryo EM
    
  • 7e8m, 7ejz, 7ek0, 7f6y, 7fbk, 7nx7, 7nx9, 7ora – hscvSpi RBD (mutant) + antibody
    
  • 7spo, 7spp – hscvSpi RBD + antibody-like
    
  • 8dlz – hscvSpi + VH – Cryo EM
    
  • 7olz, 8sk5 – hscvSpi RBD + VH
    
  • 7mjh, 7mji – hscvSpi RBD (mutant) + VH – Cryo EM
    
  • 8dm0 – hscvSpi NTD + VH – Cryo EM
    
  • 7e7x, 7ly3 – hscvSpi NTD + antibody
    
  • 7m8j, 7sww – hscvSpi NTD + antibody – Cryo EM
    
  • 7e8f – hscvSpi NTD+RBD + antibody – Cryo EM
    
  • 6zcz, 7kn6, 7kn7, 7x2k, 8cwv, 8elo, 8elp, 8elq – hscvSpi RBD + antibody + nanobody
    
  • 7y0o – hscvSpi RBD + antibody + nanobody – Cryo EM
    
  • 7dx4 – hscvSpi RBD + antibody + ACE2
    
  • 8dw3 – hscvSpi RBD + antibody + darpin – Cryo EM
    
  • 6zxn, 7lrs, 7vq0, 7z1a, 8cxq, 8cy6, 8cy7, 8cy9, 8cya, 8cyb, 8cyc, 8cyd, 8eyg, 8eyh, 8f4p – hscvSpi + nanobody - Cryo EM
    
  • 7b14, 7b17, 7mdw, 7me7, 7mej, 7n9a, 7nll, 7xrp, 8cyj – hscvSpi RBD + nanobody - Cryo EM
    
  • 7fat, 7fau, 7fbj, 7fh0, 7kgk, 7klw, 7km5, 7kn5, 7lx5, 7mfu, 7nkt, 7oao, 7oap, 7oaq, 7oau, 7oay, 7rby, 7w1s, 7wd1, 7wd2, 7x2j, 7x2l, 7x2m, 7z1b, 7z1c, 7z1d, 7z1e, 8cwu, 8h5t, 8h91, 8hr2 – hscvSpi RBD + nanobody
    
  • 7jvb, 8cxn, 8h5u – hscvSpi + nanobody
    
  • 7a25, 7a29, 7n0g, 7n0h, 7p77, 7p78, 7p79, 7p7a, 7p7b – hscvSpi + sybody - Cryo EM
    
  • 7c8v, 7c8w, 7can, 7d2z, 7d30 – hscvSpi RBD + sybody
    
  • 7rxd – hscvSpi RBD + legobody - Cryo EM
    
  • 7yco – hscvSpi RBD + repebody
    
  • 8h6f – hscvSpi + repebody – Cryo EM
    
  • 7cyv, 7deo, 7det, 7deu, 7vnb, 8bec, 8bg1, 8bg2, 8bg3, 8bg4, 8bg5, 8dce, 8juh – hscvSpi RBD + scFV
    
  • 7zce – hscvSpi + scFV – Cryo EM
    
  • 5w41 – hsc2Spi RBD + antibody
    
  • 7vng – hcv229Spi RBD + antibody
    
  • 6pz8, 5w9h, 5w9i, 5w9j, 5w9k, 5w9l, 5w9m, 5w9n, 5w9o, 5w9p – McvSpi + antibody – Cryo EM
    
  • 6j11 – McvSpi N-terminal + antibody
    
  • 5yy5, 5zxv, 4zpt, 4zpv, 5do2, 6c6y, 6c6z, 4xak, 5gmq – McvSpi RBD + antibody
    
  • 6war – McvSpi RBD + VH
    
  • 6pci, 6qd8 – ZevSpi + antibody – Cryo EM
    
• Human virus spike protein complex with ACE2
  • 6lzg, 7dmu, 7fc3, 7fc5, 7fc6, 7lo4, 7rpv, 7w6u, 7xa7 – hscvSpi RBD + ACE2
    
  • 7bh9, 7c8d, 7ddo, 7ddp, 7fdg, 7fdh, 7fdi, 7fdk, 7nxc, 7w8s, 7wse, 7wsf, 7wsg, 7zdq, 8hg0, 8t23, 8t25 – hscvSpi RBD + ACE2 – Cryo EM
    
  • 7f5r, 7sn0 – hscvSpi RBD (mutant) + ACE2
    
  • 7ydi, 8fxb, 8fxc – hscvSpi RBD + ACE2 + antibody – Cryo EM
    
  • 7l0n – hscvSpi RBD + ACE2 + antibody
    
  • 7ekh – hscvSpi RBD (mutant) + ACE2
    
  • 7eke, 7mjn, 7p19, 7sxx, 7sxy, 7sxz, 7sy0, 7sy2, 7sy4, 7sy8, 8t20, 7wa1 – hscvSpi RBD (mutant) + ACE2 – Cryo EM
    
  • 6acg, 6acj, 6ack, 6cs2, 7wsh, 8hfz – hscvSpi + ACE2 - Cryo EM
    
  • 7mjk, 7mjm, 7sy1, 7sy3, 7sy5, 7sy6, 7sy7, 8t22, 8taz – hscvSpi (mutant) + ACE2 - Cryo EM
    
  • 7y75, 7y76 – hscvSpi + ACE2 + SIT1 - Cryo EM
    
  • 2ajf – hscvSpi RBD + ACEH
    
  • 6m0j, 3d0g, 3d0h, 3d0i, 3sci, 3scj, 3sck, 3scl, 7e3j – hsc2Spi RBD + ACE2
    
  • 3kbh – hcnSpi RBD + ACE2
    
• Human virus spike protein complex with other proteins
  • 7b62 – hscvSpi NTD + biliverdin
    
  • 7x7n – hscvSpi + peptide - Cryo EM
    
  • 7l4z, 8aaa – hscvSpi RBD + peptide -
    
  • 8h3e – hscvSpi + modulator - Cryo EM
    
  • 8j1q, 8j26 – hscvSpi RBD + DNA - Cryo EM
    
  • 7c53 – hscvSpi HR1 + EK1
    
  • 6u7f, 6u7g, 6u7e – hcv229Spi RBD + aminopeptidase
    
  • 4kr0 – McvSpi RBD + CD26
    
  • 4l72 – McvSpi RBD + DPP4
    
  • 5zvk – McvSpi HR1 motif 984-1062 + peptide inhibitor
    
  • 6uye – ZevSpi + SGP – Cryo EM
    
• Human virus spike protein alpha complex
  • 7ytn – hscvSpi + antibody
    
  • 8gz5 – hsc2Spi RBD + VHH
    
  • 8dlj – hsc2Spi + ACE2 – Cryo EM
    
  • 7ekf – hsc2Spi RBD + ACE2
    
  • 8dlk – hsc2Spi RBD + ACE2 – Cryo EM
    
• Human virus spike protein beta complex
  • 7pry, 7prz, 7xeg – hscvSpi + antibody
    
  • 7q0i – hscvSpi NTD + antibody
    
  • 7fjc, 7ps0, 7ps1, 7ps2, 7ps4, 7ps5, 7ps6, 7ps7, 7q0g, 7q0h, 7x63, 7xil, 8bsf – hscvSpi RBD + antibody
    
  • 8df5 – hscvSpi RBD + antibody + ACE2
    
  • 8di5 – hscvSpi RBD + VH – Cryo EM
    
  • 7vxd, 7vxf, 7vxk, 7vxm, 8dlm – hscvSpi + ACE2 – Cryo EM
    
  • 8dln – hscvSpi RBD + ACE2 – Cryo EM
    
  • 7ekg – hscvSpi RBD + ACE2
    
• Human virus spike protein gamma complex
  • 8dlr, 8dls – hscvSpi NTD + antibody – Cryo EM
    
  • 8dlp – hscvSpi + ACE2 – Cryo EM
    
  • 7ekc, 8dlq – hscvSpi RBD + ACE2 – Cryo EM
    
  • 7wnm – hscvSpi RBD + ACE2
    
• Human virus spike protein delta complex
  • 7urq, 7urs, 8bbn, 8i5h, 8i5i – hscvSpi RBD + antibody
    
  • 7w9f, 7xdl, 7xdk – hscvSpi + antibody – Cryo EM
    
  • 7wp0, 7wro, 7wry, 7x7u, 8bcz – hscvSpi RBD + antibody – Cryo EM
    
  • 7x7d, 7x7e – hscvSpi RBD + nanobody
    
  • 8c3v – hscvSpi RBD + nanobody + antibody
    
  • 7tex – hsc2Spi + ACE2 – Cryo EM
    
  • 7vpp, 7w9i, 7wbq – hsc2Spi RBD + ACE2
    
  • 7tew – hsc2Spi RBD + ACE2 – Cryo EM
    
• Human virus spike protein epsilon complex
  • 8dlx – hscvSpi + VH – Cryo EM
    
  • 8dly – hscvSpi NTD + VH – Cryo EM
    
  • 8dlw – hscvSpi + antibody - Cryo EM
    
  • 8dlu – hscvSpi + ACE2 – Cryo EM
    
  • 8dlv – hscvSpi RBD + ACE2 – Cryo EM
    
• Human virus spike protein kappa complex
  • 7tf0, 7vx9, 7vxa, 7vxb, 7vxc – hscvSpi + ACE2 – Cryo EM
    
  • 7tez – hscvSpi RBD + ACE2 – Cryo EM
    
• Human virus spike protein omicron complex with antibody
  • 7we7, 7we8, 7we9, 7wea, 7wec, 7wi0, 7wk4, 7wk8, 7wka, 7ws6, 7xco, 7xdb, 8dm3, 8gzz, 8h3m, 8hc7, 8hc8 – hscvSpi + antibody - Cryo EM
    
  • 7web, 7wed, 7wef, 7wk0, 7wlc, 7woc, [[7wog], 7won, 7wop, 7wrl, 7wrz, 7ws2, 7ws7, 7wsa, 7wtg, 7wth, 7wtj, 7xck, 7yd1, 8hc6 – hscvSpi RBD + antibody - Cryo EM
    
  • 7x66, 7xik, 7y0w, 7zf3, 7zf5, 7zf8, 7zfa, 7zfd, 8sph – hscvSpi RBD + antibody
    
  • 7zf4, 7zfb, 7zfc, 7zfe, 7zxu, 8bh5 – hscvSpi RBD + antibody + nanobody
    
  • 8gpy – hscvSpi RBD + scFv
    
  • 7zf9, 8e1g – hscvSpi + antibody
    
  • 8h3n – hscvSpi (mutant) + antibody – Cryo EM
    
  • 8dm4 – hscvSpi NTD + antibody – Cryo EM
    
• Human virus spike protein omicron complex with ACE2
  • 7t9k, 7wbl, 7wk5, 7wk6, 7wrh, 7wvp, 7wvq, 7xch, 7y9z, 7ya0, 7yhw, 8dm5, 8dm7, 8dm9, 8hfx, 8ify, 8ifz – hscvSpi + ACE2 - Cryo EM
    
  • 7t9l, 7yj3, 7yvu, 8dm6, 8dm8, 8gry, 8h06, 8hfy – hscvSpi RBD + ACE2 - Cryo EM
    
  • 7xcp – hscvSpi + ACE2 + antibody - Cryo EM
    
  • 7wsk, 7xb0, 7ya1 – hscvSpi + ACE2
    
  • 7u0n, 7ufk, 7ufl, 7wbp, 7xaz, 7xb1, 7xby, 7xwa, 7zf7, 8asy, 8dma, 8h5c, 8if2, 8spi – hscvSpi RBD + ACE2
    
  • 7tn0 – hscvSpi RBD + ACE2 + antibody
    
• Human virus spike protein OC43 complex
  • 7sb5 – hscvSpi + antibody - Cryo EM
    
  • 7sb3, 7sbv, 7sbw, 7sbx, 7sby – hscvSpi RBD + antibody - Cryo EM
    
  • 7sb4 – hscvSpi RBD + ACE2 - Cryo EM
    
• Non-human virus spike protein
  • 4h14 – Spi lectin domain 7-290 - bovine coronavirus
    
  • 6b7n, 6bfu – pdcvSpi – porcine delta coronavirus – Cryo EM
    
  • 6u7k, 6vv5 – Spi – porcine epidemic diarrhea virus – Cryo EM
    
  • 6qfy – Spi lectin domain 15-300 - porcine hemagglutinating encephalomyelitis virus
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  • 6jhy – Spi N-terminal – camel coronavirus HKU23
    
  • 6jx7 – Spi – feline infectious peritonitis virus – Cryo EM
    
  • 1wdf, 1wdg – mhvSpi – murine hepatitis virus
    
  • 3jcl – mhvSpi – Cryo EM
    
  • 6b3o – Spi residues 718-1252 - murine coronavirus - Cryo EM
    
  • 6zgf – bcvSpi - bat coronavirus – Cryo EM
    
  • 5gyq – bcvSpi RBD
    
  • 5xgr – bcvSpi C-terminal
    
  • 7ttm, 7tty, 8j5j – bcvSpi RBD + antibody
    
  • 7p8i, 7p8j – bcvSpi RBD + ACE2
    
  • 7xsw – Spi RBD + antibody - pangolin
    
  • 6orj – Spi - Pseudomonas virus phikz164i
    
  • 2vvd, 2vve – Spi RBD - Pseudoalteromonas phage PM2
    
  • 3aqj – Spi 87-211 - Enterobacteria phage P2
    
  • [8a05j]] – Spi penton domain 1-91 - Flavobacteria phage FL-1
    
• Non-human virus spike protein complex
  • 4fsc – Spi RBD + aminopeptidase – porcine respiratory coronavirus
    
  • 7vpq – pdcvSpi RBD + aminopeptidase
    
  • 6vsj – mcvSpi + MHV-R - Cryo EM
    
  • 4qzv – bcvSpi RBD + DPP4
    
  • 4f2m – Spi 481-650 + antibody – gastroenteritis virus
    

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel