7WK4 | pdb_00007wk4

Cryo-EM structure of SARS-CoV-2 Omicron spike protein with ACE2, C1 state

• PDB DOI: https://doi.org/10.2210/pdb7WK4/pdb
• EM Map EMD-32558: EMDB EMDataResource

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


• Deposited: 2022-01-08 Released: 2022-02-02 
• Deposition Author(s): Han, W.Y., Wang, Y.F.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.69 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

• DOI: https://doi.org/10.1038/s41586-022-04581-9

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 493.04 kDa 
• Atom Count: 29,541 
• Modeled Residue Count: 3,743 
• Deposited Residue Count: 4,399 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	625	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, C, D	1,258	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 35  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: 3.69 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: 2022-02-02 
Deposition Author(s): Han, W.Y., Wang, Y.F.

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

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 2.0: 2022-03-09
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2022-05-04
  Changes: Database references
• Version 2.2: 2024-10-23
  Changes: Data collection, Structure summary
• Version 2.3: 2025-07-02
  Changes: Data collection