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- EMDB-18483: Herpes simplex virus 1 nuclear C-capsid (WT) vertices determined ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18483
TitleHerpes simplex virus 1 nuclear C-capsid (WT) vertices determined in situ
Map dataFiltered, unmasked
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: 32.0 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 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_18483.png

Downloads & links

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Map

FileDownload / File: emd_18483.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered, unmasked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.6 Å/pix.
x 92 pix.
= 791.2 Å		8.6 Å/pix.
x 60 pix.
= 516. Å		8.6 Å/pix.
x 92 pix.
= 791.2 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: 8.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.335
Minimum - Maximum-152.46884 - 89.118449999999996
Average (Standard dev.)-28.052506999999999 (±21.423432999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions609292
Spacing926092
CellA: 791.2 Å / B: 516.0 Å / C: 791.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18483_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered

Fileemd_18483_half_map_2.map
AnnotationUnfiltered
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).

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 26000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.4 sec. / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 14 / Number images used: 1170 / Software - Name: IMOD
Final angle assignmentType: OTHER / Software - Name: PEET
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 1170
FSC plot (resolution estimation)

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