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- EMDB-5576: Electron Cryo-microscopy of Chikungunya VLP in complex with neutr... -

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Basic information

Entry
Database: EMDB / ID: EMD-5576
TitleElectron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242
Map dataReconstruction of Chikungunya VLP with neutralizing antibody m242
Sample
  • Sample: Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242
  • Virus: Chikungunya virus
  • Protein or peptide: m242 antibody Fab fragment
KeywordsAlpha virus / Chikungunya VLP / neutralizing antibody m242
Biological speciesHomo sapiens (human) / Chikungunya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 15.6 Å
AuthorsSun S / Xiang Y / Rossmann MG
CitationJournal: Elife / Year: 2013
Title: Structural analyses at pseudo atomic resolution of Chikungunya virus and antibodies show mechanisms of neutralization.
Authors: Siyang Sun / Ye Xiang / Wataru Akahata / Heather Holdaway / Pankaj Pal / Xinzheng Zhang / Michael S Diamond / Gary J Nabel / Michael G Rossmann /
Abstract: A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 ...A 5.3 Å resolution, cryo-electron microscopy (cryoEM) map of Chikungunya virus-like particles (VLPs) has been interpreted using the previously published crystal structure of the Chikungunya E1-E2 glycoprotein heterodimer. The heterodimer structure was divided into domains to obtain a good fit to the cryoEM density. Differences in the T = 4 quasi-equivalent heterodimer components show their adaptation to different environments. The spikes on the icosahedral 3-fold axes and those in general positions are significantly different, possibly representing different phases during initial generation of fusogenic E1 trimers. CryoEM maps of neutralizing Fab fragments complexed with VLPs have been interpreted using the crystal structures of the Fab fragments and the VLP structure. Based on these analyses the CHK-152 antibody was shown to stabilize the viral surface, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. The CHK-9, m10 and m242 antibodies surround the receptor-attachment site, probably inhibiting infection by blocking cell attachment. DOI:http://dx.doi.org/10.7554/eLife.00435.001.
History
DepositionJan 27, 2013-
Header (metadata) releaseMar 20, 2013-
Map releaseApr 24, 2013-
UpdateApr 24, 2013-
Current statusApr 24, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2x
  • Surface level: 1
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2x
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5576.png

Downloads & links

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Map

FileDownload / File: emd_5576.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Chikungunya VLP with neutralizing antibody m242
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.22 Å/pix.
x 400 pix.
= 888. Å		2.22 Å/pix.
x 400 pix.
= 888. Å		2.22 Å/pix.
x 400 pix.
= 888. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.96484268 - 4.08135653
Average (Standard dev.)0.24649245 (±0.59243035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 888.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.222.222.22
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z888.000888.000888.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.9654.0810.246

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Supplemental data

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Sample components

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Entire : Electron Cryo-microscopy of Chikungunya VLP in complex with neutr...

EntireName: Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242
Components
  • Sample: Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242
  • Virus: Chikungunya virus
  • Protein or peptide: m242 antibody Fab fragment

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Supramolecule #1000: Electron Cryo-microscopy of Chikungunya VLP in complex with neutr...

SupramoleculeName: Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Chikungunya virus

SupramoleculeName: Chikungunya virus / type: virus / ID: 1 / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: 37997 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T / Recombinant plasmid: CMV/R
Virus shellShell ID: 1 / Name: E1E2 / Diameter: 700 Å / T number (triangulation number): 4

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Macromolecule #1: m242 antibody Fab fragment

MacromoleculeName: m242 antibody Fab fragment / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Hybridoma

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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

Concentration1 mg/mL
BufferpH: 7.4 / Details: PBS
GridDetails: 400 mesh C-flat grids
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 90 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 2 seconds before plunging.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateJan 1, 2011
Image recordingDigitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 62 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using e2boxer.
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 1728

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Atomic model buiding 1

Initial modelPDB ID:

4gq8
PDB Unreleased entry


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: EMfit
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Sumf
Output model

PDB-3j2x:
Electron Cryo-microscopy of Chikungunya VLP in complex with neutralizing antibody Fab m242

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