9IYI | pdb_00009iyi

VLP structure of Chikungunya virus complexed with C34 Fab, 2f block.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action.

Han, X.Ji, C.Tian, S.Wang, F.Cao, G.P.Li, D.Duan, X.Tong, Z.Qi, J.Wang, Q.Huang, Q.Zhan, B.D.Gao, G.F.Yan, J.

(2025) Nat Commun 16: 9682-9682

  • DOI: https://doi.org/10.1038/s41467-025-64687-2
  • Primary Citation of Related Structures:  
    9IW2, 9IXA, 9IXI, 9IYI, 9J6D

  • PubMed Abstract: 

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes febrile illness and acute or chronic arthritis. Most therapeutics are still in the pre-clinical stage. In this study, we report the isolation of two neutralizing antibodies, C34 and C37, from a convalescent patient and investigate their mechanisms of action. Both C34 and C37 exhibit high neutralizing activities in vitro and demonstrate protective effects against CHIKV in a female mouse model. Our functional and structural studies reveal a mechanism that inhibits multiple stages of the virus infection cycle. Both antibodies bind with high affinity to an epitope spanning E2, E1, and the connecting β-strands, facilitating intra- and inter-virion crosslinking. Cryo-EM structures additionally identify a minor patch located beneath the E3 binding site on E2, which is allosterically exposed upon E3 dissociation during virus maturation. Functional and structural data further suggest that binding to the CHIKV receptor, Mxra8, is obstructed due to a clash between the antibodies and the stalk region of Mxra8. Our results highlight the potential of antibody-based therapeutics against CHIKV and elucidate the mechanisms of monoclonal antibody protection.


  • Organizational Affiliation
    • CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C34 Fab, Heavy ChainA [auth S],
O [auth Q],
Q [auth O],
S [auth M]
264Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C34 Fab, Light ChainB [auth T],
P [auth R],
R [auth P],
T [auth N]
241Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CHIKV E1C [auth A],
D [auth B],
E [auth C],
F [auth D]
439Chikungunya virusMutation(s): 0 
UniProt
Find proteins for A0A286S4J4 (Chikungunya virus)
Explore A0A286S4J4 
Go to UniProtKB:  A0A286S4J4
Entity Groups  
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UniProt GroupA0A286S4J4
Glycosylation
Glycosylation Sites: 1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Structural polyproteinG [auth E],
H [auth F],
I [auth G],
J [auth H]
419Chikungunya virusMutation(s): 0 
Gene Names: CHIKVgp2
UniProt
Find proteins for D7R9A2 (Chikungunya virus)
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Go to UniProtKB:  D7R9A2
Entity Groups  
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UniProt GroupD7R9A2
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CHIKV capsid proteinK [auth I],
L [auth J],
M [auth K],
N [auth L]
151Chikungunya virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for A0A6B9KBE1 (Chikungunya virus)
Explore A0A6B9KBE1 
Go to UniProtKB:  A0A6B9KBE1
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UniProt GroupA0A6B9KBE1
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-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
6N-Glycosylation
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-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
V
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47477HI
GlyCosmos:  G47477HI
GlyGen:  G47477HI
Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
W
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D 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
X
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Y
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release