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- PDB-9u9h: Surface Tubular Element of Vaccinia Virus -

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Basic information

Entry
Database: PDB / ID: 9u9h
TitleSurface Tubular Element of Vaccinia Virus
Components
  • Mature 21 kDa protein OPG144
  • Virion membrane protein OPG140
KeywordsVIRAL PROTEIN / poxvirus / membrane 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
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Virion membrane protein OPG140 / Virion membrane protein OPG144 precursor
Similarity search - Component
Biological speciesVaccinia virus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsYu, F. / Jin, G. / Liu, Y. / Sun, Z. / Lou, Z.
Funding support China, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virion membrane protein OPG140
B: Mature 21 kDa protein OPG144
D: Virion membrane protein OPG140
E: Mature 21 kDa protein OPG144
G: Virion membrane protein OPG140
H: Mature 21 kDa protein OPG144
J: Virion membrane protein OPG140
K: Mature 21 kDa protein OPG144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,23217
Polymers116,1218
Non-polymers6,1109
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Virion membrane protein OPG140


Mass: 10003.072 Da / Num. of mol.: 4 / Source method: isolated from a natural source
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.
Source: (natural) Vaccinia virus (strain Tian Tan) / References: UniProt: P20991
#2: Protein
Mature 21 kDa protein OPG144


Mass: 19027.289 Da / Num. of mol.: 4 / Source method: isolated from a natural source
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.
Source: (natural) Vaccinia virus (strain Tian Tan) / References: UniProt: P68592
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C36H73NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DMPC, phospholipid*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Surface Tubular Element of Vaccinia Virus / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Vaccinia virus / Strain: Non-replicating vaccinia virus TianTan Strain
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -50 ° / Axial rise/subunit: 26.58 Å / Axial symmetry: C1
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 477012 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL

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