7WK0 | pdb_00007wk0

Local refine of Omicron spike bitrimer with 6m6 antibody

• PDB DOI: https://doi.org/10.2210/pdb7WK0/pdb
• EM Map EMD-32554: EMDB EMDataResource

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


• Deposited: 2022-01-08 Released: 2022-07-13 
• Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.32 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding.

Wang, Y., Zhan, W., Liu, J., Wang, Y., Zhang, X., Zhang, M., Han, L., Ma, Y., Lu, L., Wen, Y., Chen, Z., Zhao, J., Wu, F., Sun, L., Huang, J.

(2022) Cell Res 32: 862-865

• PubMed: 35768499 
• DOI: https://doi.org/10.1038/s41422-022-00684-0
• Primary Citation of Related Structures:  
  7WJY, 7WJZ, 7WK0

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Organizational Affiliation: 
• Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.
Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China.
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China. [e-mail].
Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China. [e-mail].
Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China. [e-mail].
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China. [e-mail].
Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) and Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Fifth People's Hospital, Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 139.33 kDa 
• Atom Count: 9,724 
• Modeled Residue Count: 1,264 
• Deposited Residue Count: 1,276 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6m6 heavy chain	A, D	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6m6 light chain	B, E	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C, F	198	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 15  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth C], H [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.32 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: 2022-07-13 
Deposition Author(s): Zhan, W.Q., Zhang, X., Chen, Z.G., Sun, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81900729

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2022-09-14
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection