9IZ9 | pdb_00009iz9

VLP structure of Chikungunya virus complexed with C37 Fab, 2f block.

• PDB DOI: https://doi.org/10.2210/pdb9IZ9/pdb
• EM Map EMD-61026: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Homo sapiens, Chikungunya virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-01 Released: 2025-08-06 
• Deposition Author(s): Han, X., Ji, C., Wang, F., Tian, S., Gao, F.G., Yan, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

Starting Models: experimental

Literature

VLP structure of Chikungunya virus complexed with C37 Fab, 2f block.

Han, X., Ji, C., Wang, F., Tian, S., Gao, F.G., Yan, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 20-mer - A4B4C4D4E4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 20-mer - A8B4C4D4 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - D3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 673.58 kDa 
• Atom Count: 45,105 
• Modeled Residue Count: 5,787 
• Deposited Residue Count: 6,060 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C37 Fab, Heavy chain	A [auth S], O [auth Q], Q [auth O], S [auth M]	265	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C37 Fab, Light chain	B [auth T], P [auth R], R [auth P], T [auth N]	241	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIKV E1	C [auth A], D [auth B], E [auth C], F [auth D]	439	Chikungunya virus	Mutation(s): 0
UniProt
Find proteins for A0A286S4J4 (Chikungunya virus) Explore A0A286S4J4  Go to UniProtKB:  A0A286S4J4
Glycosylation
Glycosylation Sites: 1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural polyprotein	G [auth E], H [auth F], I [auth G], J [auth H]	419	Chikungunya virus	Mutation(s): 0  Gene Names: CHIKVgp2
UniProt
Find proteins for D7R9A2 (Chikungunya virus) Explore D7R9A2  Go to UniProtKB:  D7R9A2
Glycosylation
Glycosylation Sites: 2

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIKV capsid protein	K [auth I], L [auth J], M [auth K], N [auth L]	151	Chikungunya virus	Mutation(s): 0  EC: 3.4.21.90
UniProt
Find proteins for A0A6B9KBE1 (Chikungunya virus) Explore A0A6B9KBE1  Go to UniProtKB:  A0A6B9KBE1

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	U, V, X	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-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	W	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF GlyCosmos:  G42466VF GlyGen:  G42466VF

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], EA [auth e], Y	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G10133VD GlyCosmos:  G10133VD

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], DA [auth d], Z	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	GA [auth B], HA [auth D], IA [auth E], JA [auth G]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Han, X., Ji, C., Wang, F., Tian, S., Gao, F.G., Yan, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release