9NRY | pdb_00009nry

Venezuelan Equine Encephalitis Virus in complex with the single domain antibody V2C3

• PDB DOI: https://doi.org/10.2210/pdb9NRY/pdb
• EM Map EMD-49741: EMDB EMDataResource

• Classification: Viral protein/Immune System
• Organism(s): Venezuelan equine encephalitis virus, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-14 Released: 2025-12-03 
• Deposition Author(s): Pletnev, S., Kwong, P.D., Zhou, T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Demonstration of in vivo efficacy, epitope identification, and breadth of two anti-alphavirus bispecific single domain antibodies

Gardner, C.L., Pletnev, S., Liu, J.L., Anderson, G.P., Shriver-Lake, L.C., Bylund, T., Green, C., Stephens, T., Sutton, M., Tsybovsky, Y., Roederer, M., Kwong, P.D., Zhou, T., Goldman, E.R., Burke, C.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 321.9 kDa 
• Atom Count: 19,692 
• Modeled Residue Count: 2,547 
• Deposited Residue Count: 2,934 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 envelope glycoprotein	A [auth B], B [auth G], E [auth O]	442	Venezuelan equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for A0A0C4MX98 (Venezuelan equine encephalitis virus) Explore A0A0C4MX98  Go to UniProtKB:  A0A0C4MX98

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 envelope glycoprotein	C [auth J], D [auth N], F [auth Q]	423	Venezuelan equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for A0A0C4MX98 (Venezuelan equine encephalitis virus) Explore A0A0C4MX98  Go to UniProtKB:  A0A0C4MX98

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
single domain antibody (nanobody) V2C3	G [auth X], H [auth Y], I [auth Z]	113	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev-5245
RECONSTRUCTION	cryoSPARC	4.4.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Pletnev, S., Kwong, P.D., Zhou, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release