7WVN | pdb_00007wvn

SARS-CoV-2 Omicron S-open

• PDB DOI: https://doi.org/10.2210/pdb7WVN/pdb
• EM Map EMD-32854: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-02-10 Released: 2022-03-02 
• Deposition Author(s): Li, J.W., Cong, Y.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis of receptor binding and antibody neutralization of Omicron.

Hong, Q., Han, W., Li, J., Xu, S., Wang, Y., Xu, C., Li, Z., Wang, Y., Zhang, C., Huang, Z., Cong, Y.

(2022) Nature 604: 546-552

• PubMed: 35228716 
• DOI: https://doi.org/10.1038/s41586-022-04581-9
• Primary Citation Related Structures: 
  7WK2, 7WK8, 7WK9, 7WKA, 7WVN, 7WVO, 7WVP, 7WVQ


• PubMed Abstract: 
  

  The SARS-CoV-2 Omicron variant exhibits striking immune evasion and is spreading rapidly worldwide. Understanding the structural basis of the high transmissibility and enhanced immune evasion of Omicron is of high importance. Here, using cryo-electron microscopy, we present both the closed and the open states of the Omicron spike (S) protein, which appear more compact than the counterparts of the G614 strain ¹ , potentially related to enhanced inter-protomer and S1-S2 interactions induced by Omicron residue substitution. The closed state showing dominant population may indicate a conformational masking mechanism for the immune evasion of Omicron. Moreover, we captured three states for the Omicron S-ACE2 complex, revealing that the substitutions on the Omicron RBM result in new salt bridges and hydrogen bonds, more favourable electrostatic surface properties, and an overall strengthened S-ACE2 interaction, in line with the observed higher ACE2 affinity of Omicron S than of G614. Furthermore, we determined the structures of Omicron S in complex with the Fab of S3H3, an antibody that is able to cross-neutralize major variants of concern including Omicron, elucidating the structural basis for S3H3-mediated broad-spectrum neutralization. Our findings shed light on the receptor engagement and antibody neutralization or evasion of Omicron and may also inform the design of broadly effective vaccines against SARS-CoV-2.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China. [e-mail].
CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. [e-mail].
CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. [e-mail].
State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 420.64 kDa 
• Atom Count: 24,805 
• Modeled Residue Count: 3,162 
• Deposited Residue Count: 3,774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,258	Severe acute respiratory syndrome coronavirus	Mutation(s): 34  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Li, J.W., Cong, Y.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.3: 2025-06-25
  Changes: Data collection