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- EMDB-63964: Surface Tubular Element of Vaccinia Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-63964
TitleSurface Tubular Element of Vaccinia Virus
Map dataSurface tubular element(STE) of Vaccinia virus.
Sample
  • Complex: Surface Tubular Element of Vaccinia Virus
    • Protein or peptide: Virion membrane protein OPG140
    • Protein or peptide: Mature 21 kDa protein OPG144
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Keywordspoxvirus / membrane protein / VIRAL PROTEIN
Function / homology
Function and homology information


DNA-templated transcription termination / helicase activity / hydrolase activity / viral envelope / virion membrane / DNA binding / ATP binding / membrane
Similarity search - Function
Poxvirus P21 membrane / Poxvirus P21 membrane protein / Poxvirus A14, virion envelope / Poxvirus virion envelope protein A14
Similarity search - Domain/homology
Virion membrane protein OPG140 / Virion membrane protein OPG144 precursor
Similarity search - Component
Biological speciesVaccinia virus / Vaccinia virus (strain Tian Tan)
Methodhelical reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsYu F / Jin G / Liu Y / Sun Z / Lou Z
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32300146 China
Other governmentGZNL2023A01002
CitationJournal: Mbio / Year: 2026
Title: Surface Tubular Element of Vaccinia Virus
Authors: Yu F / Jin G / Liu Y / Sun Z / Lou Z
History
DepositionMar 28, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63964.png

Downloads & links

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Map

FileDownload / File: emd_63964.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface tubular element(STE) of Vaccinia virus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 448 pix.
= 367.36 Å		0.82 Å/pix.
x 448 pix.
= 367.36 Å		0.82 Å/pix.
x 448 pix.
= 367.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-0.17821619 - 0.36519775
Average (Standard dev.)-0.00013968156 (±0.044505674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 367.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of STE.

Fileemd_63964_half_map_1.map
AnnotationHalf map of STE.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of STE.

Fileemd_63964_half_map_2.map
AnnotationHalf map of STE.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Surface Tubular Element of Vaccinia Virus

EntireName: Surface Tubular Element of Vaccinia Virus
Components
  • Complex: Surface Tubular Element of Vaccinia Virus
    • Protein or peptide: Virion membrane protein OPG140
    • Protein or peptide: Mature 21 kDa protein OPG144
  • Ligand: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Surface Tubular Element of Vaccinia Virus

SupramoleculeName: Surface Tubular Element of Vaccinia Virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Vaccinia virus / Strain: Non-replicating vaccinia virus TianTan Strain

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Macromolecule #1: Virion membrane protein OPG140

MacromoleculeName: Virion membrane protein OPG140 / type: protein_or_peptide / ID: 1
Details: Sequence reference for source organism Vaccinia virus (strain Tian Tan) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P20991.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus (strain Tian Tan)
Molecular weightTheoretical: 10.003072 KDa
SequenceString:
MDMMLMIGNY FSGVLIAGII LLILSCIFAF IDFSKSTSPT RTWKVLSIMA FILGIIITVG MLIYSMWGKH CAPHRVSGVI HTNHSDISM N

UniProtKB: Virion membrane protein OPG140

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Macromolecule #2: Mature 21 kDa protein OPG144

MacromoleculeName: Mature 21 kDa protein OPG144 / type: protein_or_peptide / ID: 2
Details: Sequence reference for source organism Vaccinia virus (strain Tian Tan) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P68592.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vaccinia virus (strain Tian Tan)
Molecular weightTheoretical: 19.027289 KDa
SequenceString:
AGVLDKDLFT EEQQQSFMPK DGGMMQNDYG GMNDYLGIFK NNDVRTLLGL ILFVLALYSP PLISILMIFI SSFLLPLTSL VITYCLVTQ MYRGGNGNTV GMSIVCIVAA VIIMAINVFT NSQIFNIISY IILFILFFAY VMNIERQDYR RSINVTIPEQ Y TCNKPYTA G

UniProtKB: Virion membrane protein OPG144 precursor

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Macromolecule #3: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 9 / Formula: PX4
Molecular weightTheoretical: 678.94 Da
Chemical component information

ChemComp-PX4:
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DMPC, phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 26.58 Å
Applied symmetry - Helical parameters - Δ&Phi: -50.00 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477012
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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