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- EMDB-18473: Subtomogram average of pseudorabies virus nuclear egress complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18473
TitleSubtomogram average of pseudorabies virus nuclear egress complex helical form (UL31/34) determined in situ
Map dataPseudorabies virus nuclear egress complex helical form determined in situ
Sample
  • Complex: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ
Keywordsin situ / nuclear egress / VIRAL PROTEIN
Biological speciesSuid herpesvirus 1 strain Kaplan
Methodsubtomogram averaging / cryo EM / Resolution: 21.0 Å
AuthorsPrazak V / Grange M / Vasishtan D
Funding support United Kingdom, Germany, 5 items
OrganizationGrant numberCountry
Wellcome Trust209250/Z/17/Z United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
German Research Foundation (DFG)390874280 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
DepositionSep 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_18473.png

Downloads & links

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Map

FileDownload / File: emd_18473.map.gz / Format: CCP4 / Size: 4.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPseudorabies virus nuclear egress complex helical form determined in situ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.55 Å/pix.
x 72 pix.
= 255.6 Å		3.55 Å/pix.
x 152 pix.
= 539.6 Å		3.55 Å/pix.
x 112 pix.
= 397.6 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: 31.399999999999999
Minimum - Maximum-149.470490000000012 - 101.320899999999995
Average (Standard dev.)-5.4637513 (±29.463584999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions15211272
Spacing11215272
CellA: 397.6 Å / B: 539.6 Å / C: 255.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unfiltered map

Fileemd_18473_additional_1.map
Annotationunfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_18473_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_18473_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ

EntireName: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ
Components
  • Complex: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ

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Supramolecule #1: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ

SupramoleculeName: Nuclear Egress Complex of Pseudorabies Virus (Kaplan strain) in situ
type: complex / ID: 1 / Parent: 0
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

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: GIF 2002
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET
Details: FSC was calculated by taking the final particles, splitting them into two groups and randomising their orientations by a maximum of 15 degrees. These two groups were then separately refined.
Number subtomograms used: 3
ExtractionNumber tomograms: 3 / Number images used: 4247 / Software - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4z3u

chain_id: C, source_name: PDB, initial_model_type: experimental model

4z3u

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross correlation

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