9KVF | pdb_00009kvf

Cryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10

• PDB DOI: https://doi.org/10.2210/pdb9KVF/pdb
• EM Map EMD-62592: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Macaca mulatta, Severe acute respiratory syndrome coronavirus 2
• Expression System: Cricetulus griseus, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-12-05 Released: 2025-08-20 
• Deposition Author(s): Sun, H., Jiang, Y., Wang, S., Zheng, Z., Li, S., Zheng, Q.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10

Sun, H., Jiang, Y., Wang, S., Zheng, Z., Li, S., Zheng, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A1B1C1D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A6B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 107.79 kDa 
• Atom Count: 6,805 
• Modeled Residue Count: 955 
• Deposited Residue Count: 984 
• Unique protein chains: 7

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2E10 light chain	A	110	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth G]	284	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 22  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
4C1 heavy chain	C [auth F]	128	Macaca mulatta	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
4C1 light chain	D [auth E]	110	Macaca mulatta	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
2E10 heavy chain	E [auth B]	122	Macaca mulatta	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
4A5 heavy chain	F [auth C]	123	Macaca mulatta	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
4A5 light chain	G [auth D]	107	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Sun, H., Jiang, Y., Wang, S., Zheng, Z., Li, S., Zheng, Q.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release