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- EMDB-9692: Cryo-EM structure of alphavirus capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-9692
TitleCryo-EM structure of alphavirus capsid
Map dataCryo-EM structure of alphavirus capsid
Sample
  • Virus: Sindbis virus
Biological speciesSindbis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsZhang X / Chen L / Wang M / Zhu D / Sun Z
CitationJournal: Nat Commun / Year: 2018
Title: Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure.
Authors: Lihong Chen / Ming Wang / Dongjie Zhu / Zhenzhao Sun / Jun Ma / Jinglin Wang / Lingfei Kong / Shida Wang / Zaisi Liu / Lili Wei / Yuwen He / Jingfei Wang / Xinzheng Zhang /
Abstract: Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. ...Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis virus, using block based reconstruction method that overcomes the heterogeneity problem. Our structural analysis identifies a number of conserved residues that play pivotal roles in the virus life cycle. We identify a hydrophobic pocket in the subdomain D of E2 protein that is stabilized by an unknown pocket factor near the viral membrane. Residues in the pocket are conserved in different alphaviruses. The pocket strengthens the interactions of the E1/E2 heterodimer and may facilitate virus assembly. Our study provides structural insights into alphaviruses that may inform the design of drugs and vaccines.
History
DepositionOct 23, 2018-
Header (metadata) releaseMar 13, 2019-
Map releaseMar 13, 2019-
UpdateMar 13, 2019-
Current statusMar 13, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9692.png

Downloads & links

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Map

FileDownload / File: emd_9692.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of alphavirus capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 384 pix.
= 518.4 Å		1.35 Å/pix.
x 384 pix.
= 518.4 Å		1.35 Å/pix.
x 384 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-9.877136999999999 - 15.5859165
Average (Standard dev.)-0.05396399 (±0.97097343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z518.400518.400518.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-9.87715.586-0.054

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Supplemental data

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Sample components

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Entire : Sindbis virus

EntireName: Sindbis virus
Components
  • Virus: Sindbis virus

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Supramolecule #1: Sindbis virus

SupramoleculeName: Sindbis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11034 / Sci species name: Sindbis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29974

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