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- EMDB-3144: Electron cryo-microscopy of chikungunya virus in complex with neu... -

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Basic information

Entry
Database: EMDB / ID: EMD-3144
TitleElectron cryo-microscopy of chikungunya virus in complex with neutralizing antibody Fab CHK265
Map dataReconstruction of chikungunya virus in complex with Fab
Sample
  • Sample: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex with murine neutralizing antibody Fab CHK265
  • Virus: Chikungunya virus
  • Protein or peptide: Fab CHK265
Keywordschikungunya virus / neutralizing antibody Fab
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / identical protein binding / plasma membrane / cytoplasm
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
Similarity search - Component
Biological speciesMus musculus (house mouse) / Chikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 16.9 Å
AuthorsFox JM / Long F / Edeling MA / Lin H / Duijl-Richter M / Fong RH / Kahle KM / Smit JM / Jin J / Simmons G ...Fox JM / Long F / Edeling MA / Lin H / Duijl-Richter M / Fong RH / Kahle KM / Smit JM / Jin J / Simmons G / Doranz BJ / Crowe JE / Fremont DH / Rossmann MG / Diamond MS
CitationJournal: Cell / Year: 2015
Title: Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress.
Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / ...Authors: Julie M Fox / Feng Long / Melissa A Edeling / Hueylie Lin / Mareike K S van Duijl-Richter / Rachel H Fong / Kristen M Kahle / Jolanda M Smit / Jing Jin / Graham Simmons / Benjamin J Doranz / James E Crowe / Daved H Fremont / Michael G Rossmann / Michael S Diamond /
Abstract: We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of ...We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O'nyong'nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern.
History
DepositionSep 4, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseNov 25, 2015-
UpdateDec 16, 2015-
Current statusDec 16, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5any
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5any
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-3144-CHI...

Downloads & links

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Map

FileDownload / File: emd_3144.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of chikungunya virus in complex with Fab
Voxel sizeX=Y=Z: 3.68 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-21.542182919999998 - 16.402292249999999
Average (Standard dev.)0.05213591 (±1.78904963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-166-166-166
Dimensions320320320
Spacing320320320
CellA=B=C: 1177.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.683.683.68
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1177.6001177.6001177.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-166-166-166
NC/NR/NS320320320
D min/max/mean-21.54216.4020.052

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Supplemental data

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Sample components

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Entire : Electron Cryo-microscopy of Chikungunya virus 181/25 in complex w...

EntireName: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex with murine neutralizing antibody Fab CHK265
Components
  • Sample: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex with murine neutralizing antibody Fab CHK265
  • Virus: Chikungunya virus
  • Protein or peptide: Fab CHK265

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Supramolecule #1000: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex w...

SupramoleculeName: Electron Cryo-microscopy of Chikungunya virus 181/25 in complex with murine neutralizing antibody Fab CHK265
type: sample / ID: 1000
Oligomeric state: one Fab binds to one envelope protein on the surface of virus
Number unique components: 2

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / Name.synonym: Chikungunya virus strain TSI-GSD-218 / NCBI-ID: 37124 / Sci species name: Chikungunya virus
Sci species strain: strain TSI-GSD-218 or vaccine strain 181/25
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Chikungunya virus strain TSI-GSD-218
Host (natural)Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES
Host systemOrganism: Chlorocebus aethiops (grivet) / Recombinant cell: Vero cells
Virus shellShell ID: 1 / Diameter: 700 Å / T number (triangulation number): 4

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Macromolecule #1: Fab CHK265

MacromoleculeName: Fab CHK265 / type: protein_or_peptide / ID: 1 / Number of copies: 240 / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse / Cell: hybridoma
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa

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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

Concentration2 mg/mL
BufferpH: 7.2 / Details: PBS
GridDetails: 400 mesh ultrathin holey carbon copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 110 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 10 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 78354 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateMar 10, 2015
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 500 / Average electron dose: 22 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.9 Å / Resolution method: OTHER / Software - Name: JSPR / Number images used: 5828
DetailsThe particles were mannually selected using the program EMAN2.

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