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- EMDB-18480: Pseudorabies virus nuclear C-capsid (WT) vertices determined in situ -

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Basic information

Entry
Database: EMDB / ID: EMD-18480
TitlePseudorabies virus nuclear C-capsid (WT) vertices determined in situ
Map dataUnmasked
Sample
  • Cell: PrV C-capsid in the nucleus of porcine epithelial-like embryonic EFN-R kidney cells
KeywordsCapsid / capsid vertex specific component / in situ / virus
Biological speciesSuid herpesvirus 1 strain Kaplan
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsMironova Y / Prazak V / Vasishtan D
Funding support United Kingdom, Germany, 5 items
OrganizationGrant numberCountry
Wellcome Trust209250/Z/17/Z United Kingdom
Wellcome Trust099683/Z/12/Z United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
German Research Foundation (DFG)390874280 Germany
German Research Foundation (DFG)453548970 Germany
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
DepositionSep 19, 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_18480.png

Downloads & links

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Map

FileDownload / File: emd_18480.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnmasked
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.1 Å/pix.
x 112 pix.
= 795.2 Å		7.1 Å/pix.
x 72 pix.
= 511.2 Å		7.1 Å/pix.
x 112 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: 7.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000279
Minimum - Maximum-0.00084221817 - 0.00091903884
Average (Standard dev.)0.00001844562 (±0.00018515573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions72112112
Spacing11272112
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: Sub-tomogram average of the nuclear A-capsids, unmasked

Fileemd_18480_additional_1.map
AnnotationSub-tomogram average of the nuclear A-capsids, unmasked
Projections & Slices
AxesZYX

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Additional map: Sub-tomogram average of the nuclear B-capsids, unmasked

Fileemd_18480_additional_2.map
AnnotationSub-tomogram average of the nuclear B-capsids, unmasked
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Unfiltered

Fileemd_18480_half_map_1.map
AnnotationUnfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered

Fileemd_18480_half_map_2.map
AnnotationUnfiltered
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PrV C-capsid in the nucleus of porcine epithelial-like embryonic ...

EntireName: PrV C-capsid in the nucleus of porcine epithelial-like embryonic EFN-R kidney cells
Components
  • Cell: PrV C-capsid in the nucleus of porcine epithelial-like embryonic EFN-R kidney cells

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Supramolecule #1: PrV C-capsid in the nucleus of porcine epithelial-like embryonic ...

SupramoleculeName: PrV C-capsid in the nucleus of porcine epithelial-like embryonic EFN-R kidney cells
type: cell / ID: 1 / Parent: 0 / Details: Cells were infected with wt PrV (Kaplan) for 10h
Source (natural)Organism: Suid herpesvirus 1 strain Kaplan

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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 / Chamber humidity: 70 % / Chamber temperature: 310.15 K / Instrument: LEICA EM GP
Details: Vitrified samples were milled using dual beam cryo-FIB-SEM (Aquilos).

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.4 sec. / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 1920
ExtractionNumber tomograms: 15 / Number images used: 1920 / Software - Name: IMOD
Final angle assignmentType: OTHER / Software - Name: PEET
FSC plot (resolution estimation)

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