9PW4 | pdb_00009pw4

Structure of V30V4 in complex with SARS-CoV-2 spike

• PDB DOI: https://doi.org/10.2210/pdb9PW4/pdb
• EM Map EMD-71899: EMDB EMDataResource

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


• Deposited: 2025-08-04 Released: 2025-11-19 
• Deposition Author(s): Wang, Y.J., Kibria, G., Wesemann, D., Chen, B.
• Funding Organization(s): Massachusetts Consortium on Pathogen Readiness (MassCPR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Affinity Maturation and light-Chain-Mediated Paratope Diversification Anticipates Viral Evolution

Dingus, J., Yoo, D.K., Kumar, S., Kibria, G., Wang, Y.J., Allahyari, Z., Chen, J., Saghei, S., Chen, B., Wesemann, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 172.4 kDa 
• Atom Count: 8,160 
• Modeled Residue Count: 1,058 
• Deposited Residue Count: 1,564 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	684	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V30V4 FAB LIGHT CHAIN	B [auth D]	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SP1-77 FAB LIGHT CHAIN	C [auth F]	213	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
V30V4 FAB HEAVY CHAIN	D [auth C]	226	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SP1-77 FAB HEAVY CHAIN	E	225	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
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	F [auth B]	4		N/A
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Wang, Y.J., Kibria, G., Wesemann, D., Chen, B.

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Funding Organization	Location	Grant Number
Massachusetts Consortium on Pathogen Readiness (MassCPR)	United States	--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release