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- PDB-9iw2: Chikungunya virus E protein complexed with C37 Fab -

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Basic information

Entry
Database: PDB / ID: 9iw2
TitleChikungunya virus E protein complexed with C37 Fab
Components
  • C37 Heavy Chain
  • C37 light chain
  • CHIKV E1
  • Togavirin
KeywordsANTIVIRAL PROTEIN / chikungunya / antibody
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell membrane / viral capsid / host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane ...T=4 icosahedral viral capsid / host cell membrane / viral capsid / host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsQi, J. / Han, X. / Wang, F. / Tian, S. / Gao, F.G. / Yan, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action.
Authors: Xiaonan Han / Chengfan Ji / Siyu Tian / Fengze Wang / Guo-Ping Cao / Ding Li / Xiaomin Duan / Zhou Tong / Jianxun Qi / Qihui Wang / Qingrui Huang / Bing-Dong Zhan / George Fu Gao / Jinghua Yan /
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 ...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.
History
DepositionJul 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: CHIKV E1
H: C37 Heavy Chain
L: C37 light chain
P: Togavirin


Theoretical massNumber of molelcules
Total (without water)146,4214
Polymers146,4214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.087, 118.995, 228.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHIKV E1


Mass: 46030.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Homo sapiens (human) / References: UniProt: A4L787
#2: Antibody C37 Heavy Chain


Mass: 28556.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody C37 light chain


Mass: 25950.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Protein Togavirin / CHIKV p62


Mass: 45882.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Homo sapiens (human) / References: UniProt: C8YZ73, togavirin
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES, Sodium hydroxide, PEG 20000 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26345 / % possible obs: 99.3 % / Redundancy: 6.1 % / CC1/2: 0.966 / CC star: 0.991 / Net I/σ(I): 3.5
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 1693 / Rsym value: 0.247 / % possible all: 64.87

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→46.85 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1207 4.99 %
Rwork0.2218 --
obs0.2246 24165 91.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9007 0 0 0 9007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049283
X-RAY DIFFRACTIONf_angle_d0.84812651
X-RAY DIFFRACTIONf_dihedral_angle_d8.5811283
X-RAY DIFFRACTIONf_chiral_restr0.0531412
X-RAY DIFFRACTIONf_plane_restr0.0061636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.3316970.29231783X-RAY DIFFRACTION65
3.33-3.480.3281100.26872011X-RAY DIFFRACTION73
3.48-3.660.33671270.26942435X-RAY DIFFRACTION88
3.66-3.890.29741290.23872640X-RAY DIFFRACTION96
3.89-4.190.27361490.22742723X-RAY DIFFRACTION98
4.19-4.620.27521430.19672770X-RAY DIFFRACTION99
4.62-5.280.2271410.19132808X-RAY DIFFRACTION100
5.28-6.650.25781280.22412836X-RAY DIFFRACTION100
6.65-46.850.2771830.20912952X-RAY DIFFRACTION100

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