[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

TitleIn situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque.
Journal, issue, pagesNat Microbiol, Vol. 10, Issue 7, Page 1723-1740, Year 2025
Publish dateJul 1, 2025
AuthorsTina Drobnič / Eli J Cohen / Thomas Calcraft / Mona Alzheimer / Kathrin Froschauer / Sarah Svensson / William H Hoffmann / Nanki Singh / Sriram G Garg / Louie D Henderson / Trishant R Umrekar / Andrea Nans / Deborah Ribardo / Francesco Pedaci / Ashley L Nord / Georg K A Hochberg / David R Hendrixson / Cynthia M Sharma / Peter B Rosenthal / Morgan Beeby /
PubMed AbstractThe bacterial flagellar motor, which spins a helical propeller for propulsion, has undergone evolutionary diversification across bacterial species, often involving the addition of structures ...The bacterial flagellar motor, which spins a helical propeller for propulsion, has undergone evolutionary diversification across bacterial species, often involving the addition of structures associated with increasing torque for motility in viscous environments. Understanding how such structures function and have evolved is hampered by challenges in visualizing motors in situ. Here we developed a Campylobacter jejuni minicell system for in situ cryogenic electron microscopy imaging and single-particle analysis of its motor, one of the most complex flagellar motors known, to subnanometre resolution. Focusing on the large periplasmic structures which are essential for increasing torque, our structural data, interpreted with molecular models, show that the basal disk comprises concentric rings of FlgP. The medial disk is a lattice of PflC with PflD, while the proximal disk is a rim of PflB attached to spokes of PflA. PflAB dimerization is essential for proximal disk assembly, recruiting FliL to scaffold more stator complexes at a wider radius which increases torque. We also acquired insights into universal principles of flagellar torque generation. This in situ approach is broadly applicable to other membrane-residing bacterial molecular machines.
External linksNat Microbiol / PubMed:40595286 / PubMed Central
MethodsEM (single particle) / EM (subtomogram averaging)
Resolution7.9 - 81.0 Å
Structure data

EMDB-16723: Wild-type Campylobacter jejuni flagellar motor, in situ
Method: EM (single particle) / Resolution: 9.36 Å

EMDB-16724: Periplasmic scaffold of the Campylobacter jejuni flagellar motor
PDB-9hmf: Periplasmic scaffold of the Campylobacter jejuni flagellar motor (alpha carbon trace)
Method: EM (single particle) / Resolution: 7.9 Å

EMDB-17415: Campylobacter jejuni flagellar motor, pflC deletion
Method: EM (subtomogram averaging) / Resolution: 80.0 Å

EMDB-17416: Campylobacter jejuni flagellar motor, pflD deletion
Method: EM (subtomogram averaging) / Resolution: 58.0 Å

EMDB-17417: Campylobacter jejuni flagellar motor, truncated PflA (d16-168)
Method: EM (subtomogram averaging) / Resolution: 57.5 Å

EMDB-17419: Campylobacter jejuni flagellar motor, FlgQ-mCherry fusion
Method: EM (subtomogram averaging) / Resolution: 81.0 Å

Source
  • campylobacter jejuni (Campylobacter)
KeywordsSTRUCTURAL PROTEIN / molecular machines / flagellar motor / molecular evolution / in situ / scaffold / MOTOR PROTEIN

+
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