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- EMDB-17974: Pseudorabies virus cytosolic C-capsid (US3 KO) vertices determine... -

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Basic information

Entry
Database: EMDB / ID: EMD-17974
TitlePseudorabies virus cytosolic C-capsid (US3 KO) vertices determined in situ
Map dataSharpened map of cytosolic PRV C-capsid vertices determined in situ
Sample
  • Virus: Suid herpesvirus 1 strain Kaplan
Keywordscapsid vertex specific component / in situ / cytosol / VIRUS
Biological speciesSuid herpesvirus 1 strain Kaplan
Methodsubtomogram averaging / cryo EM / Resolution: 31.0 Å
AuthorsPrazak V / Grange M / Vasishtan D
Funding support United Kingdom, Germany, 7 items
OrganizationGrant numberCountry
Wellcome Trust209250/Z/17/ Z United Kingdom
Wellcome Trust209250/Z/17/Z United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
German Research Foundation (DFG)390874280 Germany
German Research Foundation (DFG)453548970 Germany
Wellcome Trust107806/Z/15/Z United Kingdom
Wellcome Trust099683/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: NECing goes: flexibility of the herpesvirus nuclear egress complex
Authors: Prazak V / Hagen C / Vasishtan D / Mironova Y / Laugks U / Jensen Y / Sanders S / Heumann JM / Bosse JB / Klupp B / Mettenleiter TC / Grange M / Grunewald K
History
DepositionJul 18, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17974.png

Downloads & links

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Map

FileDownload / File: emd_17974.map.gz / Format: CCP4 / Size: 27.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of cytosolic PRV C-capsid vertices determined in situ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.55 Å/pix.
x 224 pix.
= 795.2 Å		3.55 Å/pix.
x 144 pix.
= 511.2 Å		3.55 Å/pix.
x 224 pix.
= 795.2 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: 3.55 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 39.200000000000003
Minimum - Maximum-231.466720000000009 - 186.354340000000008
Average (Standard dev.)-5.3167796 (±35.007275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144224224
Spacing224144224
CellA: 795.2 Å / B: 511.19998 Å / C: 795.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of cytosolic PRV B-capsid vertices determined in situ

Fileemd_17974_additional_1.map
AnnotationSharpened map of cytosolic PRV B-capsid vertices determined in situ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of cytosolic PRV A-capsid vertices determined in situ

Fileemd_17974_additional_2.map
AnnotationSharpened map of cytosolic PRV A-capsid vertices determined in situ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered map of cytosolic PRV C-capsid vertices determined in situ

Fileemd_17974_additional_3.map
AnnotationUnfiltered map of cytosolic PRV C-capsid vertices determined in situ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of cytosolic PRV C-capsid vertices determined in situ

Fileemd_17974_half_map_1.map
AnnotationHalf-map 1 of cytosolic PRV C-capsid vertices determined in situ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of cytosolic PRV C-capsid vertices determined in situ

Fileemd_17974_half_map_2.map
AnnotationHalf-map 2 of cytosolic PRV C-capsid vertices determined in situ
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Suid herpesvirus 1 strain Kaplan

EntireName: Suid herpesvirus 1 strain Kaplan
Components
  • Virus: Suid herpesvirus 1 strain Kaplan

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Supramolecule #1: Suid herpesvirus 1 strain Kaplan

SupramoleculeName: Suid herpesvirus 1 strain Kaplan / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 33703 / Sci species name: Suid herpesvirus 1 strain Kaplan / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: kevin

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.4 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 4 / Number images used: 1065 / Software - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 31.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 1065
FSC plot (resolution estimation)

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