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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 / Chen M
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: Nat Commun / Year: 2026
Title: Cryogenic electron tomography reveals herpesvirus capsid assembly intermediates inside the cell nucleus.
Authors: Stefan L Oliver / Muyuan Chen / Leeya Engel / Corey W Hecksel / Xueting Zhou / Michael F Schmid / Ann M Arvin / Wah Chiu /
Abstract: Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been ...Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been characterized, but their roles in herpesvirus replication remain controversial. The status of the capsid vertex-specific component (CVSC), essential for capsid stability and dsDNA packaging and retention, is also unclear. By integrating cryogenic focused ion beam milling with electron tomography and subtomogram averaging, we derive atomic models for all protein components, including the CVSC, across different herpesvirus capsid types within infected cell nuclei. Focused classification of pentonal vertex densities reveal differences in CVSC occupancy between genome-filled capsids and capsids lacking dsDNA, highlight structural heterogeneity and providing insight into distinct capsid assembly stages in situ. These intra-nuclear findings redefine the maturation model of herpesvirus capsid assembly, advancing the understanding of herpesvirus replication, and demonstrate the effectiveness of in situ electron imaging by studying virus assembly within host cells.
History
DepositionMar 24, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 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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