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- EMDB-30477: Cryo-EM structure of Chikungunya virus in complex with Fab fragme... -

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Basic information

Entry
Database: EMDB / ID: EMD-30477
TitleCryo-EM structure of Chikungunya virus in complex with Fab fragments of mAb CHK-263
Map data
Sample
  • Complex: Chikungunya virus in complex with Fab fragments of mAb CHK-263
    • Organelle or cellular component: Chikungunya virus
      • Protein or peptide: E1 glycoprotein
      • Protein or peptide: E2 glycoprotein
      • Protein or peptide: Capsid protein
    • Organelle or cellular component: CHK-263 Fab
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Fab light chain
Keywordsvirus / Fab / complex / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / viral translational frameshifting / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / viral translational frameshifting / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / 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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsZhou QF / Fox JM / Earnest JT / Ng TS / Kim AS / Fibriansah G / Kostyuchenko VA / Shu B / Diamond MS / Lok SM
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Other government Singapore
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structural basis of Chikungunya virus inhibition by monoclonal antibodies.
Authors: Qun Fei Zhou / Julie M Fox / James T Earnest / Thiam-Seng Ng / Arthur S Kim / Guntur Fibriansah / Victor A Kostyuchenko / Jian Shi / Bo Shu / Michael S Diamond / Shee-Mei Lok /
Abstract: Chikungunya virus (CHIKV) is an emerging viral pathogen that causes both acute and chronic debilitating arthritis. Here, we describe the functional and structural basis as to how two anti-CHIKV ...Chikungunya virus (CHIKV) is an emerging viral pathogen that causes both acute and chronic debilitating arthritis. Here, we describe the functional and structural basis as to how two anti-CHIKV monoclonal antibodies, CHK-124 and CHK-263, potently inhibit CHIKV infection in vitro and in vivo. Our in vitro studies show that CHK-124 and CHK-263 block CHIKV at multiple stages of viral infection. CHK-124 aggregates virus particles and blocks attachment. Also, due to antibody-induced virus aggregation, fusion with endosomes and egress are inhibited. CHK-263 neutralizes CHIKV infection mainly by blocking virus attachment and fusion. To determine the structural basis of neutralization, we generated cryogenic electron microscopy reconstructions of Fab:CHIKV complexes at 4- to 5-Å resolution. CHK-124 binds to the E2 domain B and overlaps with the Mxra8 receptor-binding site. CHK-263 blocks fusion by binding an epitope that spans across E1 and E2 and locks the heterodimer together, likely preventing structural rearrangements required for fusion. These results provide structural insight as to how neutralizing antibody engagement of CHIKV inhibits different stages of the viral life cycle, which could inform vaccine and therapeutic design.
History
DepositionAug 27, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cvz
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cvz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30477.png

Downloads & links

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Map

FileDownload / File: emd_30477.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 500 pix.
= 855. Å		1.71 Å/pix.
x 500 pix.
= 855. Å		1.71 Å/pix.
x 500 pix.
= 855. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-15.326957 - 20.296375000000001
Average (Standard dev.)0.00028643795 (±0.9999954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 855.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z855.000855.000855.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS500500500
D min/max/mean-15.32720.2960.000

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Supplemental data

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Sample components

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Entire : Chikungunya virus in complex with Fab fragments of mAb CHK-263

EntireName: Chikungunya virus in complex with Fab fragments of mAb CHK-263
Components
  • Complex: Chikungunya virus in complex with Fab fragments of mAb CHK-263
    • Organelle or cellular component: Chikungunya virus
      • Protein or peptide: E1 glycoprotein
      • Protein or peptide: E2 glycoprotein
      • Protein or peptide: Capsid protein
    • Organelle or cellular component: CHK-263 Fab
      • Protein or peptide: Fab heavy chain
      • Protein or peptide: Fab light chain

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Supramolecule #1: Chikungunya virus in complex with Fab fragments of mAb CHK-263

SupramoleculeName: Chikungunya virus in complex with Fab fragments of mAb CHK-263
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Chikungunya virus

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Supramolecule #3: CHK-263 Fab

SupramoleculeName: CHK-263 Fab / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 47.503016 KDa
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KNLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVTAYAN GDHAVTVKDA K FIVGPMSS ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KNLPDYSCKV FTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVTAYAN GDHAVTVKDA K FIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNMP ISIDIPEAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVAI IKY AASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHPPKRT TVYYPASHTT LGVQ DISAT AMSWVQKITG GVGLVVAVAA LILIVVLCVS FSRH

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Macromolecule #2: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 46.904559 KDa
SequenceString: NFNVYKATRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERAGLF VRTSAPCTI TGTIGHFILA RCPKGETLTV GFTDSRKISH SCTHPFHHDP PVIGREKFHS RPQHGKELPC STYVQSTAAT T EEIEVHMP ...String:
NFNVYKATRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERAGLF VRTSAPCTI TGTIGHFILA RCPKGETLTV GFTDSRKISH SCTHPFHHDP PVIGREKFHS RPQHGKELPC STYVQSTAAT T EEIEVHMP PDTPDHTLMS QQSGNVKITV NGQTVRYKCN CGGSNEGLTT TDKVINNCKV DQCHAAVTNH KKWQYNSPLV PR NAELGDR KGKIHIPFPL ANVTCRVPKA RNPTVTYGKN QVIMLLYPDH PTLLSYRNMG EEPNYQEEWV MHKKEVVLTV PTE GLEVTW GNNEPYKYWP QLSTNGTAHG HPHEIILYYY ELYPTMTVVV VSVATFILLS MVGMAAGMCM CARRRCITPY ELTP GATVP FLLSLICCIR TAKA

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Chikungunya virus
Molecular weightTheoretical: 16.428607 KDa
SequenceString:
NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW

UniProtKB: Structural polyprotein

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Macromolecule #4: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.87267 KDa
SequenceString: VQLQQSGAEL VKPGASVKIS CKASGYAFSS YWMNWVKQRP GKGLEWIGQI YPGDGDTNYN GKFKGKATLT ADKSSSTAYM QLSSLTSED SAVYFCARGG LTIDYWGQGT TLTVSSAKTT APSVYPLAPV CGGTTGSSVT LGCLVKGYFP EPVTLTWNSG S LSSGVHTF ...String:
VQLQQSGAEL VKPGASVKIS CKASGYAFSS YWMNWVKQRP GKGLEWIGQI YPGDGDTNYN GKFKGKATLT ADKSSSTAYM QLSSLTSED SAVYFCARGG LTIDYWGQGT TLTVSSAKTT APSVYPLAPV CGGTTGSSVT LGCLVKGYFP EPVTLTWNSG S LSSGVHTF PALLQSGLYT LSSSVTVTSN TWPSQTITCN VAHPASSTKV DKKIESRR

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Macromolecule #5: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.38157 KDa
SequenceString: DIVLTQSPAT LSVTPGDSVS LSCRASQSIS DNLHWYQQKS HESPGLLIKY ASQSISGIPS RFSGSGSGTD FTLSINSVET EDFGMYFCQ QSNSWPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVLTQSPAT LSVTPGDSVS LSCRASQSIS DNLHWYQQKS HESPGLLIKY ASQSISGIPS RFSGSGSGTD FTLSINSVET EDFGMYFCQ QSNSWPYTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNE

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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: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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