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- EMDB-5577: Electron cryo-microscopy of Chikungunya virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5577
TitleElectron cryo-microscopy of Chikungunya virus
Map dataIcosahedral reconstruction of Chikungunya virus.
Sample
  • Sample: Chikungunya VLP
  • Virus: Chikungunya virus
KeywordsE1-E2 glycoprotein / nucleocapsid protein / transmembrane helix
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 / 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 ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / identical protein 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
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsSun SY / Xiang Y / Wataru A / Holdaway H / Pal P / Zhang XZ / Diamond MS / Nabel GJ / 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 28, 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: 1.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2w
  • Surface level: 1.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5577_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5577.map.gz / Format: CCP4 / Size: 506.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of Chikungunya virus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 324 pix.
= 359.64 Å		1.11 Å/pix.
x 648 pix.
= 719.28 Å		1.11 Å/pix.
x 648 pix.
= 719.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1 / Movie #1: 1.1
Minimum - Maximum-0.64053935 - 12.825798989999999
Average (Standard dev.)0.3046951 (±0.94753766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-324-3240
Dimensions648648324
Spacing648648324
CellA: 719.28 Å / B: 719.28 Å / C: 359.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z648648324
origin x/y/z0.0000.0000.000
length x/y/z719.280719.280359.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-324-3240
NC/NR/NS648648324
D min/max/mean-0.64112.8260.305

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Supplemental data

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Sample components

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Entire : Chikungunya VLP

EntireName: Chikungunya VLP
Components
  • Sample: Chikungunya VLP
  • Virus: Chikungunya virus

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Supramolecule #1000: Chikungunya VLP

SupramoleculeName: Chikungunya VLP / type: sample / ID: 1000 / Number unique components: 1

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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 293F
Virus shellShell ID: 1 / Name: E1E2 / Diameter: 750 Å / T number (triangulation number): 4

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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 / Details: PBS
GridDetails: 400 mesh copper grid (1.2 um hole)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 2 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification
DateJan 1, 2011
Image recordingCategory: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 1532 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, Frealign / Number images used: 36236

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Atomic model buiding 1

Initial modelPDB ID:

3n43

SoftwareName: EMfit
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-3j2w:
Electron cryo-microscopy of Chikungunya virus

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