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- EMDB-49469: VZV portal cryo-ET reconstruction. -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49469
TitleVZV portal cryo-ET reconstruction.
Map dataVZV portal cryo-ET reconstruction.
Sample
  • Virus: Human alphaherpesvirus 3 (Varicella-zoster virus)
KeywordsVaricella-zoster virus / capsid / cryo-ET / cryo-FIB / VIRUS
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Methodsubtomogram averaging / cryo EM / Resolution: 22.9 Å
AuthorsOliver SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 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
DepositionFeb 26, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49469.png

Downloads & links

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Map

FileDownload / File: emd_49469.map.gz / Format: CCP4 / Size: 106.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVZV portal cryo-ET reconstruction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.88 Å/pix.
x 30 pix.
= 206.4 Å		6.88 Å/pix.
x 30 pix.
= 206.4 Å		6.88 Å/pix.
x 30 pix.
= 206.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3
Minimum - Maximum-17.166495999999999 - 17.915520000000001
Average (Standard dev.)0.60288864 (±1.5857693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions303030
Spacing303030
CellA=B=C: 206.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49469_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: VZV portal cryo-ET reconstruction low pass filtered 15A.

Fileemd_49469_additional_1.map
AnnotationVZV portal cryo-ET reconstruction low pass filtered 15A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VZV portal cryo-ET reconstruction half map odd.

Fileemd_49469_half_map_1.map
AnnotationVZV portal cryo-ET reconstruction half map odd.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VZV portal cryo-ET reconstruction half map even.

Fileemd_49469_half_map_2.map
AnnotationVZV portal cryo-ET reconstruction half map even.
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 / Macromolecule list: #1-#7 / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / Sci species strain: pOka / Virus type: VIRION / Virus isolate: SPECIES / 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 statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.923 sec. / Average electron dose: 1.481 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 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: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.01) / Number subtomograms used: 109
ExtractionNumber tomograms: 22 / Number images used: 109
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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