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- EMDB-8760: Capsid of Pseudorabies virus imaged in intact virions -

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Basic information

Entry
Database: EMDB / ID: 8760
TitleCapsid of Pseudorabies virus imaged in intact virions
Map dataunfiltered map
SampleSuid herpesvirus 1 (strain Becker):
virus
SourceSuid herpesvirus 1 (strain Becker)
Methodsingle particle reconstruction / cryo EM / 4.9 Å resolution
AuthorsLiu YT / Jiang J / Bohannon KP / Dai X / Luxton GW / Hui WH / Bi GQ / Smith GA / Zhou ZH
CitationJournal: J. Gen. Virol. / Year: 2017
Title: A pUL25 dimer interfaces the pseudorabies virus capsid and tegument.
Authors: Yun-Tao Liu / Jiansen Jiang / Kevin Patrick Bohannon / Xinghong Dai / G W Gant Luxton / Wong Hoi Hui / Guo-Qiang Bi / Gregory Allan Smith / Z Hong Zhou
DateDeposition: Jun 8, 2017 / Header (metadata) release: Jul 19, 2017 / Map release: Nov 1, 2017 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8760.map.gz (map file in CCP4 format, 1 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1024 pix
1.61 Å/pix.
= 1648.64 Å
1024 pix
1.61 Å/pix.
= 1648.64 Å
1024 pix
1.61 Å/pix.
= 1648.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.61 Å
Density
Contour Level:0.006 (by author), 0.006 (movie #1):
Minimum - Maximum-0.02073158 - 0.032964323
Average (Standard dev.)-0.0004562682 (0.0029965595)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions102410241024
Origin-512.-512.-512.
Limit511.511.511.
Spacing102410241024
CellA=B=C: 1648.64 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.611.611.61
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z1648.6401648.6401648.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-512-512-512
NC/NR/NS102410241024
D min/max/mean-0.0210.033-0.000

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Supplemental data

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Sample components

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Entire Suid herpesvirus 1 (strain Becker)

EntireName: Suid herpesvirus 1 (strain Becker) / Number of components: 1

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Component #1: virus, Suid herpesvirus 1 (strain Becker)

VirusName: Suid herpesvirus 1 (strain Becker) / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Suid herpesvirus 1 (strain Becker)
Source (natural)Host Species: Sus scrofa (pig)
Shell #1Name of element: Capsid / Diameter: 1250.0 Å / T number(triangulation number): 16

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1830

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 13537
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body

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