Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 401.03 kDa 
• Atom Count: 16317 
• Modelled Residue Count: 2208 
• Deposited Residue Count: 3609 
• Unique protein chains: 1

5WRG

SARS-CoV spike glycoprotein

• PDB DOI: 10.2210/pdb5WRG/pdb
• EM Map EMD-6679:EMDBEMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-12-01 Released: 2017-01-11 
• Deposition Author(s): Gui, M., Song, W., Xiang, Y., Wang, X.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding.

Gui, M., Song, W., Zhou, H., Xu, J., Chen, S., Xiang, Y., Wang, X.

(2017) Cell Res 27: 119-129

• PubMed: 28008928 
• DOI: 10.1038/cr.2016.152
• Primary Citation of Related Structures:  
  5WRG, 5XLR


• PubMed Abstract: 
  

The global outbreak of SARS in 2002-2003 was caused by the infection of a new human coronavirus SARS-CoV. The infection of SARS-CoV is mediated mainly through the viral surface glycoproteins, which consist of S1 and S2 subunits and form trimer spikes on the envelope of the virions. Here we report the ectodomain structures of the SARS-CoV surface spike trimer in different conformational states determined by single-particle cryo-electron microscopy. The conformation 1 determined at 4.3 Å resolution is three-fold symmetric and has all the three receptor-binding C-terminal domain 1 (CTD1s) of the S1 subunits in "down" positions. The binding of the "down" CTD1s to the SARS-CoV receptor ACE2 is not possible due to steric clashes, suggesting that the conformation 1 represents a receptor-binding inactive state. Conformations 2-4 determined at 7.3, 5.7 and 6.8 Å resolutions are all asymmetric, in which one RBD rotates away from the "down" position by different angles to an "up" position. The "up" CTD1 exposes the receptor-binding site for ACE2 engagement, suggesting that the conformations 2-4 represent a receptor-binding active state. This conformational change is also required for the binding of SARS-CoV neutralizing antibodies targeting the CTD1. This phenomenon could be extended to other betacoronaviruses utilizing CTD1 of the S1 subunit for receptor binding, which provides new insights into the intermediate states of coronavirus pre-fusion spike trimer during infection.

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Organizational Affiliation: 

Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1203	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 1  Gene Names: S, 2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594  Go to UniProtKB:  P59594

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-01 
• Released Date: 2017-01-11 
Deposition Author(s): Gui, M., Song, W., Xiang, Y., Wang, X.

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-04-05
  Changes: Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Other