9KVJ | pdb_00009kvj

Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (local refinement)

• PDB DOI: https://doi.org/10.2210/pdb9KVJ/pdb
• EM Map EMD-62596: EMDB EMDataResource

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


• Deposited: 2024-12-05 Released: 2025-12-10 
• Deposition Author(s): Sun, H., Jiang, Y., Li, S., Zheng, Q.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (local refinement)

Sun, H., Jiang, Y., Li, S., Zheng, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 47.93 kDa 
• Atom Count: 3,342 
• Modeled Residue Count: 418 
• Deposited Residue Count: 422 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of nAb 1C4	A [auth C]	119	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of nAb 1C4	B [auth D]	107	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth G]	196	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 17  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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.82 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: 2025-12-10 
Deposition Author(s): Sun, H., Jiang, Y., Li, S., Zheng, Q.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release