[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

Title architecture of the Tad pilus machine in .
Journal, issue, pagesmBio, Vol. 17, Issue 5, Page e0011126, Year 2026
Publish dateMay 13, 2026
AuthorsJames Iarocci / Gregory B Whitfield / Ryu F Williston / Michael R Wozny / Kaustuv Basu / John F Presley / Courtney K Ellison / Yves V Brun / Shuaiqi Guo /
PubMed AbstractThe tight adherence (Tad) pilus is a broadly distributed and evolutionarily distinct subclass of type IV pili that mediate cell adhesion, biofilm formation, predation, and surface sensing in many ...The tight adherence (Tad) pilus is a broadly distributed and evolutionarily distinct subclass of type IV pili that mediate cell adhesion, biofilm formation, predation, and surface sensing in many bacteria, including , , , and . Tad pili undergo cycles of extension and retraction powered by a cell-envelope-embedded nanomachine. Despite their biological importance, the architecture and assembly mechanism of the Tad pilus system remain poorly understood. Although cryo-electron tomography (cryo-ET) has elucidated the architectures of other type IV pilus systems, no intact Tad machine structure has previously been reported. Here, we use cryo-ET and subtomogram averaging to resolve the architecture of the Tad pilus within the bacterial cell envelope. A three-dimensional classification further reveals multiple assembly intermediates, and integrative modeling incorporating AlphaFold3 predictions helps define the spatial arrangement of all core components. The resulting structural framework gives insight into the stepwise assembly process of the Tad pilus machine. Altogether, our results provide an architectural model of the Tad pilus machine, establishing a foundation for understanding homologous systems across a broad range of bacteria.
IMPORTANCE: Investigating the Tad pilus nanomachine in a genetically tractable, non-pathogenic organism like provides a powerful model for elucidating the architecture and functional dynamics of this widespread system. Insights gained from studying the Tad machinery can improve our understanding of related Tad pilus systems in pathogenic bacteria such as , where Tad pili are a key determinant of biofilm formation and chronic infection. Additionally, the remarkable functional diversity of Tad systems, ranging from surface sensing in to bacterial predation in , highlights their broad biological relevance. By revealing the architecture of the Tad pilus biosynthetic machinery, this study advances our understanding of a major class of bacterial nanomachines and may thus provide structural insights that could inform the development of new therapeutic strategies targeting pilus-mediated virulence.
External linksmBio / PubMed:41879311 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution38.91 - 56.82 Å
Structure data

EMDB-73615: Sub-tomogram averaged structure of the non-piliated Tad machine in Caulobacter crescentus
Method: EM (subtomogram averaging) / Resolution: 42.02 Å

EMDB-73632: Sub-tomogram averaged structure of the piliated Tad machine in Caulobacter crescentus
Method: EM (subtomogram averaging) / Resolution: 56.82 Å

EMDB-73646: Sub-tomogram averaged structure of the Tad pilus secretin in Caulobacter crescentus
Method: EM (subtomogram averaging) / Resolution: 38.91 Å

Source
  • Caulobacter vibrioides (bacteria)

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more