7WK3 | pdb_00007wk3

SARS-CoV-2 Omicron S-open

• PDB DOI: https://doi.org/10.2210/pdb7WK3/pdb
• EM Map EMD-32557: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-01-08 Released: 2022-01-26 
• 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

Structural basis for ACE2 engagement and antibody evasion and neutralization of SARS-Co-2 Omicron varient

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 401.74 kDa 
• Atom Count: 24,805 
• Modeled Residue Count: 3,162 
• Deposited Residue Count: 3,615 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,205	Severe acute respiratory syndrome coronavirus 2	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: 2022-01-26 
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: 2022-01-26
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Structure summary
• Version 1.2: 2025-06-18
  Changes: Data collection