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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: To Be Published
Title: In situ structure of the poxvirus portal complex
Authors: Calcraft T / Hernandez-Gonzalez M / Nans A / Rosenthal PB / Way M
History
DepositionOct 22, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 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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