9DQX | pdb_00009dqx

Structure of western equine encephalitis virus CBA87 VLP

• PDB DOI: https://doi.org/10.2210/pdb9DQX/pdb
• EM Map EMD-47117: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Western equine encephalitis virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-24 Released: 2025-03-26 
• Deposition Author(s): Abraham, J., Fan, X., Li, W.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of western equine encephalitis virus CBA87 VLP

Abraham, J., Fan, X., Li, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A4B4C4 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 443.74 kDa 
• Atom Count: 30,900 
• Modeled Residue Count: 3,995 
• Deposited Residue Count: 4,024 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural polyprotein	A [auth J], D, E [auth G], F [auth A]	437	Western equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for P13897 (Western equine encephalitis virus) Explore P13897  Go to UniProtKB:  P13897
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural polyprotein	B [auth K], G [auth E], H, I [auth B]	406	Western equine encephalitis virus	Mutation(s): 0
UniProt
Find proteins for P13897 (Western equine encephalitis virus) Explore P13897  Go to UniProtKB:  P13897
Glycosylation
Glycosylation Sites: 2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	C [auth L], J [auth F], K [auth I], L [auth C]	163	Western equine encephalitis virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for P13897 (Western equine encephalitis virus) Explore P13897  Go to UniProtKB:  P13897

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	M [auth J], N [auth K], O [auth K], P [auth D], Q [auth G], R [auth A], S [auth E], T [auth E], U [auth H], V [auth H], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 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: 2025-03-26 
Deposition Author(s): Abraham, J., Fan, X., Li, W.

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

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Data collection