Sandbox 3001

Function The viral spike protein (Spi) binds the virus to its host cell via the cell's receptor: angiotensin-converting enzyme 2 (ACE2). The trimeric 2019-nCoV Spi binds to ACE2 at least 10 times more tightly than SARS coronavirus . Disease Numerous viral diseases are causing world-shattering consequences and the current pandemic of CoVID-2019 is the recent one. Relevance The spike protein is a key target for potential therapies and diagnostics. Various antibodies are currently being tested as potential CoVID-2019 antiviral treatment. Structural highlights The SARS-CoV Spi receptor binding domain complex with its cellular receptor - ACE2 - shows the interactions (shown for one of the two monomers) to ACE2 "hot spot".

spinqualitylabelsall models Human coronavirus NL63 spike glycoprotein (magenta) complex with its ligand ACE2 (green) (PDB code 3kbh) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

3D Structures of spike protein3D Structures of spike protein

Updated on 13-April-2020

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• Human virus spike protein; Domain Receptor Binding Domain (RBD) 318-510; HR1 910-1054; HR2 1162-1286
  • 5wrg, 5xlr, 6acc, 6acd – hscvSpi – human SARS-CoV – Cryo EM
    
  • 6crv, 6crw, 6crx, 6crz, 6cs0, 6cs1 – hscvSpi (mutant) – Cryo EM
    
  • 1wnc – hscvSpi HR1 motif
    
  • 2fxp – hscvSpi HR2 motif - NMR
    
  • 2ghv – hscvSpi RBD
    
  • 5xjk – hscvSpi 758-821 - NMR
    
  • 1wyy – hscvSpi 885-1189
    
  • 1zv7, 1zv8, 1zva, 1zvb – hscvSpi 1150-1193
    
  • 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
    
  • 5gnb, 5kwb – Spi RBD - human beta coronavirus
    
  • 6cv0 – Spi – infectious bronchitis coronavirus – Cryo EM
    
  • 5fyn – Spi ectodomain - puumala virus - Cryo EM
    
  • 5x59, 5x5c, 5x5f, 6q04, 6q05, 6q06, 6q07 – McvSpi – MERS coronavirus virus – Cryo EM
    
  • 5x4r, 5x4s – McvSpi N-terminal – Cryo EM
    
  • 5vyh – McvSpi N-terminal
    
  • 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 complex
  • 2ajf – hscvSpi RBD + ACEH
    
  • 6nb6, 6nb7 – hscvSpi + antibody - Cryo EM
    
  • 2ghw, 3bgf, 2dd8 – hscvSpi RBD + antibody
    
  • 6lzg – hscvSpi RBD + ACE2
    
  • 6acg, 6acj, 6ack, 6cs2 – hscvSpi + ACE2 - Cryo EM
    
  • 6atk, 6u7f, 6u7g, 6u7e – hcv229Spi RBD + aminopeptidase
    
  • 6m0j, 3d0g, 3d0h, 3d0i, 3sci, 3scj, 3sck, 3scl – hsc2Spi RBD + ACE2
    
  • 5w41 – hsc2Spi RBD + antibody
    
  • 3kbh – hcnSpi RBD + ACE2
    
  • 4kr0 – McvSpi RBD + CD26
    
  • 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
    
  • 4l72 – McvSpi RBD + DPP4
    
  • 5zvk – McvSpi HR1 motif 984-1062 + peptide inhibitor
    
  • 6pci, 6qd8 – ZevSpi + antibody – Cryo EM
    
  • 6uye – ZevSpi + SGP – Cryo EM
    
• Non-human virus spike protein
  • 4h14 – Spi lectin domain 7-290 - bovine coronavirus
    
  • 6b7n, 6bfu – Spi – 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 – mcvSpi residues 718-1252 - murine coronavirus - Cryo EM
    
  • 5gyq – bcvSpi RBD - bat coronavirus
    
  • 5xgr – bcvSpi C-terminal
    
  • 6orj – Spi - Pseudomonas virus phikz164i
    
  • 2vvd, 2vve – Spi RBD - Pseudoalteromonas phage PM2
    
  • 3aqj – Spi 87-211 - Enterobacteria phage P2
    
• Non-human virus spike protein complex
  • 4fsc – Spi RBD + aminopeptidase – porcine respiratory coronavirus
    
  • 6vsj – mcvSpi + MHV-R - Cryo EM
    
  • 4qzv – bcvSpi RBD + DPP4