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- EMDB-9331: Pre-fusion protein gB revealed on VSV by cryo electron tomography... -

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Basic information

Entry
Database: EMDB / ID: 9331
TitlePre-fusion protein gB revealed on VSV by cryo electron tomography with Volta phase plate
Map dataIn situ structure of VSV gB in the prefusion conformation
SampleVesicular stomatitis Indiana virus:
virus
SourceVesicular stomatitis Indiana virus
Methodsubtomogram averaging / cryo EM / 40 Å resolution
AuthorsZhu S / Jiayan Z
CitationJournal: PLoS Pathog. / Year: 2018
Title: Different functional states of fusion protein gB revealed on human cytomegalovirus by cryo electron tomography with Volta phase plate.
Authors: Zhu Si / Jiayan Zhang / Sakar Shivakoti / Ivo Atanasov / Chang-Lu Tao / Wong H Hui / Kang Zhou / Xuekui Yu / Weike Li / Ming Luo / Guo-Qiang Bi / Z Hong Zhou
DateDeposition: Nov 12, 2018 / Header (metadata) release: Nov 28, 2018 / Map release: Nov 28, 2018 / Last update: Dec 19, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.68
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.68
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9331.map.gz (map file in CCP4 format, 865 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
5.2 Å/pix.
= 312. Å
60 pix
5.2 Å/pix.
= 312. Å
60 pix
5.2 Å/pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.2 Å
Density
Contour Level:3.68 (by author), 3.68 (movie #1):
Minimum - Maximum-21.288550999999998 - 18.496414000000001
Average (Standard dev.)-1.0103261 (3.2582753)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin-30.0-30.0-30.0
Limit29.029.029.0
Spacing606060
CellA=B=C: 312.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-21.28918.496-1.010

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Supplemental data

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Sample components

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Entire Vesicular stomatitis Indiana virus

EntireName: Vesicular stomatitis Indiana virus / Number of components: 1

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Component #1: virus, Vesicular stomatitis Indiana virus

VirusName: Vesicular stomatitis Indiana virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
MassTheoretical: 171 kDa
SpeciesSpecies: Vesicular stomatitis Indiana virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 5
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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