[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

TitleStructural insights into the Thermus thermophilus type IV pilus machinery assembling two distinct pili.
Journal, issue, pagesCommun Biol, Vol. 9, Issue 1, Year 2026
Publish dateMar 31, 2026
AuthorsAlexander Neuhaus / Mathew McLaren / Michail N Isupov / Matthew Gaines / Emma Buzzard / Mateusz Sikora / Cyril Hanus / Bertram Daum / Beate Averhoff / Vicki A M Gold /
PubMed AbstractType IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus ...Type IV pili are long, filamentous structures that extend from bacterial cell surfaces, enabling cells to respond to changing environments and facilitating genome plasticity. Thermus thermophilus HB27 produces two different type IV pili, each exhibiting distinct structural and functional properties. Here, we combine cryo-electron tomography, mutagenesis, and AlphaFold predictions to generate hypothetical in situ models of the T. thermophilus type IV pilus assembly machinery. Using single-particle cryo-electron microscopy, we determine structures of both filament types, enabling modelling of their surface glycans. Molecular dynamics simulations further reveal the flexibility of these glycans on extrusion. Integration of the filament structures with our hypothetical model of the assembly machinery offers a framework for further dissecting T4P architecture and biogenesis.
External linksCommun Biol / PubMed:41917195 / PubMed Central
MethodsEM (helical sym.) / EM (subtomogram averaging)
Resolution2.4 - 180.0 Å
Structure data

EMDB-18588, PDB-8qqd:
CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
Method: EM (helical sym.) / Resolution: 2.4 Å

EMDB-18593, PDB-8qqj:
CryoEM structure of the type IV pilin PilA5 from Thermus thermophilus
Method: EM (helical sym.) / Resolution: 2.63 Å

EMDB-56468: Structure of the type IV pilus machinery from Thermus thermophilus in the open state (C13 symmetry)
Method: EM (subtomogram averaging) / Resolution: 115.0 Å

EMDB-56469: Structure of the type IV pilus machinery from Thermus thermophilus in the open state (C6 symmetry)
Method: EM (subtomogram averaging) / Resolution: 180.0 Å

EMDB-56470: Structure of the type IV pilus machinery from Thermus thermophilus in the closed state (C13 symmetry)
Method: EM (subtomogram averaging) / Resolution: 66.0 Å

EMDB-56471: Structure of the type IV pilus machinery from Thermus thermophilus in the closed state (C6 symmetry)
Method: EM (subtomogram averaging) / Resolution: 140.0 Å

Chemicals

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

ChemComp-MG:
Unknown entry

Source
  • thermus thermophilus hb27 (bacteria)
  • thermus thermophilus (bacteria)
KeywordsPROTEIN FIBRIL / Type IV pilin glycosylation / twitching motility

+
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