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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: To Be Published
Title: NECing goes: flexibility of the herpesvirus nuclear egress complex
Authors: Prazak V / Mironova Y / Vasishtan D / Hagen C / Laugks U / Jensen Y / Sanders S / Heumann JM / Bosse JB / Klupp B / Mettenleiter TC / Grange M / Grunewald K
History
DepositionSep 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_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
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
Specialist opticsEnergy filter - Name: GIF 2002
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: 3 / Number images used: 4247 / Software - Name: PEET
Final angle assignmentType: OTHER / Software - Name: PEET
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
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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