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- EMDB-61168: Structure of Chikungunya virus infectious particles, 2f block. -

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Basic information

Entry
Database: EMDB / ID: EMD-61168
TitleStructure of Chikungunya virus infectious particles, 2f block.
Map data
Sample
  • Virus: Chikungunya virus
    • Protein or peptide: chikungunya E3
    • Protein or peptide: chikungunya virus E1
    • Protein or peptide: chikungunya E2
    • Protein or peptide: CHIKV capsid protein
Keywordschikungunya / VIRUS
Function / homology
Function and homology information


T=4 icosahedral viral capsid / 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 nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...T=4 icosahedral viral capsid / 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 nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / 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
Structural polyprotein / p130 / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsHan X / Ji C / Wang F / Tian S / Gao FG / Yan J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92369202 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
DepositionAug 15, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61168.png

Downloads & links

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Map

FileDownload / File: emd_61168.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.4804328 - 0.89619404
Average (Standard dev.)0.0066644987 (±0.042746294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61168_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61168_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Chikungunya virus

EntireName: Chikungunya virus
Components
  • Virus: Chikungunya virus
    • Protein or peptide: chikungunya E3
    • Protein or peptide: chikungunya virus E1
    • Protein or peptide: chikungunya E2
    • Protein or peptide: CHIKV capsid protein

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: chikungunya E3

MacromoleculeName: chikungunya E3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 6.217213 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PVMCLLANTT FPCSQPPCTP CCYEKEPEET LRMLEDNVMR PGYYQLLQAS LTCSP

UniProtKB: p130

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Macromolecule #2: chikungunya virus E1

MacromoleculeName: chikungunya virus E1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 47.497906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESEDVYANTQ LVLQRPSAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AMNCAVGNMP ISIDIPDAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVAI IKY AASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHPPKDH IVNYPASHTT LGVQ DISVT AMSWVQKITG GVGLVVAVAA LILIVVLCVS FSRH

UniProtKB: Structural polyprotein

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Macromolecule #3: chikungunya E2

MacromoleculeName: chikungunya E2 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 46.548082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP ...String:
NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP PDTPDRTLMS QQSGNVKITV NSQTVRYKCN CGDSNEGLTT TDKVINNCKV DQCHAAVTNH KKWQYNSPLV PR NAELGDR KGKVHIPFPL ANVTCRVPKA RNPTVTYGKN QVIMLLYPDH PTLLSYRNMG EEPNYQEEWV THKKEIRLTV PTE GLEVTW GNNEPYKYWP QLSTNGTAHG HPHEIILYYY ELYPTMTVVV VSVASFVLLS MVGVAVGMCM CARRRCITPY ELTP GATVP FLLSLICCI

UniProtKB: Structural polyprotein

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Macromolecule #4: CHIKV capsid protein

MacromoleculeName: CHIKV capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 16.428607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW

UniProtKB: Structural polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jo8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1618503
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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