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- EMDB-18484: Herpes simplex virus 1 nuclear egress complex (WT) determined in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18484
TitleHerpes simplex virus 1 nuclear egress complex (WT) determined in situ from perinuclear vesicles
Map dataHerpes simplex virus-1 nuclear egress complex determined in situ
Sample
  • Virus: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
KeywordsCapsid / capsid vertex specific component / in situ / virus
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 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: 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 19, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18484.png

Downloads & links

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Map

FileDownload / File: emd_18484.map.gz / Format: CCP4 / Size: 768.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHerpes simplex virus-1 nuclear egress complex determined in situ
Voxel sizeX=Y=Z: 8.484 Å
Density
Contour LevelBy AUTHOR: 2.07
Minimum - Maximum-138.185489999999987 - 31.064475999999999
Average (Standard dev.)-31.43873 (±11.767434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions486464
Spacing644864
CellA: 542.976 Å / B: 407.232 Å / C: 542.976 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unfiltered map at bin4

Fileemd_18484_additional_1.map
AnnotationUnfiltered map at bin4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_18484_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_18484_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 : Human alphaherpesvirus 1

EntireName: Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Components
  • Virus: Human alphaherpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1: Human alphaherpesvirus 1

SupramoleculeName: Human alphaherpesvirus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10298 / Sci species name: Human alphaherpesvirus 1 / Sci species strain: 17 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 310.15 K
Details: Vitrified samples were milled using dual beam cryo-FIB-SEM (Aquilos).
DetailsVero cells were infected with HSV1 (strain 17) at MOI 30 and incubated for 15 h

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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: 5.0 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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 8526
ExtractionNumber tomograms: 4 / Number images used: 8526 / Software - Name: IMOD
Final angle assignmentType: OTHER / Software - Name: PEET
FSC plot (resolution estimation)

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