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- EMDB-55457: Subtomogram average of the Vaccinia virus (WR) portal complex in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55457
TitleSubtomogram average of the Vaccinia virus (WR) portal complex in isolated virus cores
Map data
Sample
  • Complex: Portal complex with surrounding palisade trimers
    • Complex: Portal complex
    • Complex: Palisade trimers
Keywordsportal complex / morphogenesis / assembly / translation / VIRAL PROTEIN
Biological speciesVaccinia virus WR
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 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_55457.png

Downloads & links

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Map

FileDownload / File: emd_55457.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 200 pix.
= 312. Å		1.56 Å/pix.
x 200 pix.
= 312. Å		1.56 Å/pix.
x 200 pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.10293808 - 0.17983961
Average (Standard dev.)-0.00000000000034 (±0.017144952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55457_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55457_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55457_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Portal complex with surrounding palisade trimers

EntireName: Portal complex with surrounding palisade trimers
Components
  • Complex: Portal complex with surrounding palisade trimers
    • Complex: Portal complex
    • Complex: Palisade trimers

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Supramolecule #1: Portal complex with surrounding palisade trimers

SupramoleculeName: Portal complex with surrounding palisade trimers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Vaccinia virus WR / Strain: A36-YdF

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Supramolecule #2: Portal complex

SupramoleculeName: Portal complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Vaccinia virus WR

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Supramolecule #3: Palisade trimers

SupramoleculeName: Palisade trimers / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Vaccinia virus WR

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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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / 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: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.5 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
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: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 7118
ExtractionNumber tomograms: 625 / Number images used: 11366 / Method: Template matching / Software:
Namedetails
PyTom
UCSF ChimeraXArtiaX
RELION
/ Details: Pytom template matching
CTF correctionSoftware - Name: RELION / Software - details: Aretomo2 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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