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- EMDB-49886: Cryo-ET map of the VZV capsid 3-fold axis. -

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Basic information

Entry
Database: EMDB / ID: EMD-49886
TitleCryo-ET map of the VZV capsid 3-fold axis.
Map dataCryo-ET map of the VZV capsid 3-fold axis.
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
KeywordsVaricella zoster virus / capsid / 3-fold axis / VIRUS
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsubtomogram averaging / cryo EM / Resolution: 8.4 Å
AuthorsOliver SL / Muyuan C
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI020459 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI159375 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM139166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21MH125285 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI15937502 United States
National Institutes of Health/Office of the DirectorS10OD021600 United States
CitationJournal: To Be Published
Title: Cryo-ET map of the VZV capsid 3-fold axis.
Authors: Oliver SL
History
DepositionMar 24, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49886.png

Downloads & links

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Map

FileDownload / File: emd_49886.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET map of the VZV capsid 3-fold axis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.44 Å/pix.
x 192 pix.
= 660.48 Å		3.44 Å/pix.
x 192 pix.
= 660.48 Å		3.44 Å/pix.
x 192 pix.
= 660.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-14.051349 - 15.770438
Average (Standard dev.)0.053239428 (±0.90858227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 660.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49886_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-ET halfmap1 of the VZV capsid 3-fold axis.

Fileemd_49886_half_map_1.map
AnnotationCryo-ET halfmap1 of the VZV capsid 3-fold axis.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-ET halfmap2 of the VZV capsid 3-fold axis.

Fileemd_49886_half_map_2.map
AnnotationCryo-ET halfmap2 of the VZV capsid 3-fold axis.
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 3

EntireName: Human alphaherpesvirus 3 (Varicella-zoster virus)
Components
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)

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Supramolecule #1: Human alphaherpesvirus 3

SupramoleculeName: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 0.974 sec. / Average electron dose: 1.577 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 3804
ExtractionNumber tomograms: 69 / Number images used: 3804
CTF correctionSoftware - Name: EMAN2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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