9IXA | pdb_00009ixa

Cryo-EM structure of chikungunya virus glycoprotein E1-E2 with C34 Fab.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHIKV E2406Chikungunya virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for C8YZ73 (Chikungunya virus)
Explore C8YZ73 
Go to UniProtKB:  C8YZ73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8YZ73
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CHIKV E1441Chikungunya virusMutation(s): 0 
UniProt
Find proteins for D1GCB6 (Chikungunya virus)
Explore D1GCB6 
Go to UniProtKB:  D1GCB6
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UniProt GroupD1GCB6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C34 Fab, Heavy ChainC [auth H]268Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
C34 Fab, Light ChainD [auth L]241Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTcryoSPARC
MODEL REFINEMENTRELION

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: 2025-11-19
    Type: Initial release