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- EMDB-55456: In situ subtomogram average of the Vaccinia virus (WR) portal com... -

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Basic information

Entry
Database: EMDB / ID: EMD-55456
TitleIn situ subtomogram average of the Vaccinia virus (WR) portal complex in cytoplasmic cores
Map data
Sample
  • Virus: Vaccinia virus WR
KeywordsPortal complex / DNA helicase / VIRUS
Biological speciesVaccinia virus WR
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsCalcraft T / Hernandez-Gonzalez M / Nans A / Rosenthal PB / Way M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Nature / Year: 2026
Title: In situ structure of the poxvirus portal complex.
Authors: Thomas Calcraft / Miguel Hernandez-Gonzalez / Michael Way / Peter B Rosenthal /
Abstract: Poxviruses are a family of large, complex double-stranded DNA viruses that includes human pathogens such as variola-the cause of smallpox-and monkeypox. Recent outbreaks of mpox underscore the need ...Poxviruses are a family of large, complex double-stranded DNA viruses that includes human pathogens such as variola-the cause of smallpox-and monkeypox. Recent outbreaks of mpox underscore the need for a better understanding of poxvirus biology. Poxvirus assembly is a conserved process that involves the formation of a biconcave core inside the membrane of the maturing virus. Here we use cryo-electron tomography combined with subtomogram averaging and structure prediction to determine the structure and composition of the portal complex-a pore that spans the core wall-in vaccinia virus, the prototypical poxvirus. The hexameric complex consists of the E8, E6 and L3 proteins, which are conserved across poxviruses and essential for mRNA release during the establishment of infection. E6, which is also required for virus assembly, forms the central chamber of the portal and interacts with the surrounding core wall. A hexamer of E8 attaches to the exterior side of E6. L3, a target of TRIM5α-mediated restriction, binds as a hexamer of dimers to the interior side. Furthermore, the viral helicase D5, which is required for genome release from cores, associates with cytoplasmic cores during infection by docking onto the exterior E8 rim of the portal complex. We propose that the portal complex represents an attractive target for the development of anti-poxvirus therapeutics.
History
DepositionOct 22, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55456.png

Downloads & links

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Map

FileDownload / File: emd_55456.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
4.31 Å/pix.
x 128 pix.
= 551.68 Å		4.31 Å/pix.
x 128 pix.
= 551.68 Å		4.31 Å/pix.
x 128 pix.
= 551.68 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.104
Minimum - Maximum-0.452135 - 0.44622007
Average (Standard dev.)-0.000000000001611 (±0.06057781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 551.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55456_msk_1.map
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Half map: #2

Fileemd_55456_half_map_1.map
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Half map: #1

Fileemd_55456_half_map_2.map
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Sample components

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Entire : Vaccinia virus WR

EntireName: Vaccinia virus WR
Components
  • Virus: Vaccinia virus WR

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Supramolecule #1: Vaccinia virus WR

SupramoleculeName: Vaccinia virus WR / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10254 / Sci species name: Vaccinia virus WR / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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 R3.5/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Details: 45mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 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: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 11600
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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 191
ExtractionNumber tomograms: 8 / Number images used: 677 / Software - Name: PyTom
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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