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- EMDB-17975: Pseudorabies virus primary enveloped (perinuclear) C-capsid (US3 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17975
TitlePseudorabies virus primary enveloped (perinuclear) C-capsid (US3 KO) vertices determined in situ
Map dataSharpened map of primary enveloped particle (perinuclear) C-capsid vertices
Sample
  • Virus: Suid herpesvirus 1 strain Kaplan
Keywordsin situ / perinucleus / VIRUS
Biological speciesSuid herpesvirus 1 strain Kaplan
Methodsubtomogram averaging / cryo EM / Resolution: 23.0 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: Nat Microbiol / Year: 2024
Title: Molecular plasticity of herpesvirus nuclear egress analysed in situ.
Authors: Vojtěch Pražák / Yuliia Mironova / Daven Vasishtan / Christoph Hagen / Ulrike Laugks / Yannick Jensen / Saskia Sanders / John M Heumann / Jens B Bosse / Barbara G Klupp / Thomas C ...Authors: Vojtěch Pražák / Yuliia Mironova / Daven Vasishtan / Christoph Hagen / Ulrike Laugks / Yannick Jensen / Saskia Sanders / John M Heumann / Jens B Bosse / Barbara G Klupp / Thomas C Mettenleiter / Michael Grange / Kay Grünewald /
Abstract: The viral nuclear egress complex (NEC) allows herpesvirus capsids to escape from the nucleus without compromising the nuclear envelope integrity. The NEC lattice assembles on the inner nuclear ...The viral nuclear egress complex (NEC) allows herpesvirus capsids to escape from the nucleus without compromising the nuclear envelope integrity. The NEC lattice assembles on the inner nuclear membrane and mediates the budding of nascent nucleocapsids into the perinuclear space and their subsequent release into the cytosol. Its essential role makes it a potent antiviral target, necessitating structural information in the context of a cellular infection. Here we determined structures of NEC-capsid interfaces in situ using electron cryo-tomography, showing a substantial structural heterogeneity. In addition, while the capsid is associated with budding initiation, it is not required for curvature formation. By determining the NEC structure in several conformations, we show that curvature arises from an asymmetric assembly of disordered and hexagonally ordered lattice domains independent of pUL25 or other viral capsid vertex components. Our results advance our understanding of the mechanism of nuclear egress in the context of a living cell.
History
DepositionJul 18, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17975.png

Downloads & links

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Map

FileDownload / File: emd_17975.map.gz / Format: CCP4 / Size: 27.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of primary enveloped particle (perinuclear) C-capsid vertices
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: 26.199999999999999
Minimum - Maximum-213.335530000000006 - 172.77788000000001
Average (Standard dev.)-5.027217 (±33.733466999999997)
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: Unfiltered map of primary enveloped particle (perinuclear) C-capsid...

Fileemd_17975_additional_1.map
AnnotationUnfiltered map of primary enveloped particle (perinuclear) C-capsid vertices
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of primary enveloped particle (perinuclear) A-,...

Fileemd_17975_additional_2.map
AnnotationSharpened map of primary enveloped particle (perinuclear) A-, B- and partially filled capsid vertices
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of primary enveloped particle (perinuclear)...

Fileemd_17975_half_map_1.map
AnnotationHalf map 1 of primary enveloped particle (perinuclear) C-capsid vertices
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of primary enveloped particle (perinuclear)...

Fileemd_17975_half_map_2.map
AnnotationHalf map 1 of primary enveloped particle (perinuclear) C-capsid vertices
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 20
ExtractionNumber tomograms: 20 / Number images used: 3950 / Software - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
FSC plot (resolution estimation)

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