9IW2 | pdb_00009iw2

Chikungunya virus E protein complexed with C37 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9IW2

This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 146.42 kDa 
  • Atom Count: 9,007 
  • Modeled Residue Count: 1,171 
  • Deposited Residue Count: 1,340 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHIKV E1A [auth F]432Chikungunya virusMutation(s): 0 
UniProt
Find proteins for Q1H8W5 (Chikungunya virus)
Explore Q1H8W5 
Go to UniProtKB:  Q1H8W5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1H8W5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
C37 Heavy ChainB [auth H]265Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
C37 light chainC [auth L]237Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
TogavirinD [auth P]406Chikungunya virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for Q1H8W5 (Chikungunya virus)
Explore Q1H8W5 
Go to UniProtKB:  Q1H8W5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1H8W5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.087α = 90
b = 118.995β = 90
c = 228.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
HKL-2000data reduction
PHENIXphasing

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: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references