[English] 日本語
Yorodumi
- PDB-9u9h: Surface Tubular Element of Vaccinia Virus -

+
Open data


ID or keywords:

Loading...

-
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


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
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: 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, 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
Revision 1.1Mar 18, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Apr 1, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.3Apr 22, 2026Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 1.3Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / Item: _citation.journal_volume / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more