9BBN | pdb_00009bbn

Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9

• PDB DOI: https://doi.org/10.2210/pdb9BBN/pdb
• EM Map EMD-44423: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Chikungunya virus, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-04-06 Released: 2025-10-08 
• Deposition Author(s): Su, G.C., Galaz-Montoya, J.G., Pintilie, G., Jin, J., Chiu, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryogenic Electron Microscopy Reveals Dual-Inhibition Mechanisms and Explains the Differential Neutralization Potency of Two anti-CHIKV Antibodies

Su, G.C., Galaz-Montoya, J.G., Pintilie, G., Jin, J., Chiu, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 24-mer - A4B4C4D4E4F4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 24-mer - A7B4C4D4E4F1 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - C3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2D2E2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 663.07 kDa 
• Atom Count: 46,492 
• Modeled Residue Count: 6,060 
• Deposited Residue Count: 6,060 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 glycoprotein	A [auth U], B [auth W], C [auth X], X [auth V]	60	Chikungunya virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for D2KBQ2 (Chikungunya virus) Explore D2KBQ2  Go to UniProtKB:  D2KBQ2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 glycoprotein	D [auth C], F [auth A], J [auth B], S [auth D]	439	Chikungunya virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for Q88628 (Chikungunya virus) Explore Q88628  Go to UniProtKB:  Q88628

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 glycoprotein	E [auth G], G [auth E], M [auth F], V [auth H]	419	Chikungunya virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for Q88628 (Chikungunya virus) Explore Q88628  Go to UniProtKB:  Q88628

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of C9	H [auth M], K [auth O], P [auth Q], T [auth S]	234	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of C9	I [auth N], L [auth P], Q [auth R], U [auth T]	212	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	N [auth J], O [auth K], R [auth I], W [auth L]	151	Chikungunya virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for Q88628 (Chikungunya virus) Explore Q88628  Go to UniProtKB:  Q88628

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Su, G.C., Galaz-Montoya, J.G., Pintilie, G., Jin, J., Chiu, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103832

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release