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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


helicase activity / DNA-templated transcription termination / 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: Architecture of surface tubular element of poxvirus.
Authors: Fengxi Yu / Ge Jin / Yixiao Liu / Zhenyu Liu / Jingxuan Yao / Junbo Wang / Daoxin Xie / Zihe Rao / Liming Yan / Yan Zhang / Zixian Sun / Zhiyong Lou /
Abstract: Poxviruses are large enveloped DNA viruses that cause severe human infectious diseases. The mature virion of poxvirus is covered with dense surface tubular elements (STEs), which play a role in ...Poxviruses are large enveloped DNA viruses that cause severe human infectious diseases. The mature virion of poxvirus is covered with dense surface tubular elements (STEs), which play a role in assembly progress of mature virions (MVs) and inhibit host cell protein synthesis. However, the composition and assembly of STEs remain unclear. Cryo-electron microscopy (cryo-EM) has proven to be a powerful technique for determining the structure of proteins from complex biological samples. By integrating high-resolution cryo-EM maps with mass spectrometry, we reveal that STEs are helically assembled from two transmembrane proteins, A14 and A17, which bind to phospholipid molecules and form the tubular scaffold along the poxviral membrane. Extensive intermolecular interactions, including A14 dimers and A14-A17 complexes, drive the remarkable structural stability of STEs. Structural analysis further emphasizes the reticulon-like properties of A17, which promote membrane curvature and stabilize the tubular architecture. These results provide novel insights into the STE assembly, morphogenesis, and surface organization of poxviruses, offering valuable information for the development of vaccines and antiviral strategies against poxvirus infections.IMPORTANCESurface tubular elements (STEs) are critical components of poxvirus mature virions and play a role in suppressing host cell protein synthesis. In this study, we isolated and purified STEs from native poxvirus virions and subsequently determined their core composition and high-resolution architecture. We identified that STE is mainly composed of membrane proteins A14 and A17, along with phospholipid molecules. Within the repeat structural unit of STE, A14 proteins form two homodimers within the repeating unit, with A17 monomers flanking either side. Phospholipid molecules are distributed within the A14-A14 and A14-A17 interfaces. Our study not only revealed the molecular structures of A14 and A17 but also further emphasized that the reticulon-like and highly oligomerized characteristics of A17 provide membrane curvature, while the A14-A17-phospholipid network stabilizes the tubular structure. We proposed a hypothetical model that A17 drives changes in viral membrane curvature during maturation. These findings enhance our understanding of poxvirus biology and may guide therapeutic strategies against poxvirus infections.
History
DepositionMar 28, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 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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