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- EMDB-9329: Post-fusion protein gB revealed on human cytomegalovirus by cryo ... -

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Basic information

Entry
Database: EMDB / ID: 9329
TitlePost-fusion protein gB revealed on human cytomegalovirus by cryo electron tomography with Volta phase plate
Map dataIn situ structure of HCMV gB in the postfusion conformation
SampleHuman herpesvirus 5 strain AD169:
virus
SourceHuman herpesvirus 5 strain AD169
Methodsubtomogram averaging / cryo EM / 26 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: 2.63
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.63
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9329.map.gz (map file in CCP4 format, 563 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
52 pix
5.2 Å/pix.
= 270.4 Å
52 pix
5.2 Å/pix.
= 270.4 Å
52 pix
5.2 Å/pix.
= 270.4 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:2.63 (by author), 2.63 (movie #1):
Minimum - Maximum-2.0014248 - 6.3890944
Average (Standard dev.)0.00000039603887 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions525252
Origin-26.0-26.0-26.0
Limit25.025.025.0
Spacing525252
CellA=B=C: 270.4 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/z525252
origin x/y/z0.0000.0000.000
length x/y/z270.400270.400270.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-26-26-26
NC/NR/NS525252
D min/max/mean-2.0016.3890.000

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Supplemental data

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Sample components

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Entire Human herpesvirus 5 strain AD169

EntireName: Human herpesvirus 5 strain AD169 / Number of components: 1

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Component #1: virus, Human herpesvirus 5 strain AD169

VirusName: Human herpesvirus 5 strain AD169 / Class: VIRION / Empty: Yes / Enveloped: Yes / Isolate: OTHER
MassTheoretical: 300 kDa
SpeciesSpecies: Human herpesvirus 5 strain AD169

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
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: 11
3D reconstructionResolution: 26 Å / Resolution method: FSC 0.143 CUT-OFF

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