[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

TitleCryo-EM Structure of the Flagellar Motor Complex from sp. TCA20.
Journal, issue, pagesBiomolecules, Vol. 15, Issue 3, Year 2025
Publish dateMar 18, 2025
AuthorsSakura Onoe / Tatsuro Nishikino / Miki Kinoshita / Norihiro Takekawa / Tohru Minamino / Katsumi Imada / Keiichi Namba / Jun-Ichi Kishikawa / Takayuki Kato /
PubMed AbstractThe bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. ...The bacterial flagellum, a complex nanomachine composed of numerous proteins, is utilized by bacteria for swimming in various environments and plays a crucial role in their survival and infection. The flagellar motor is composed of a rotor and stator complexes, with each stator unit functioning as an ion channel that converts flow from outside of cell membrane into rotational motion. sp. TCA20 was discovered in a hot spring, and a structural analysis was conducted on the stator complex using cryo-electron microscopy to elucidate its function. Two of the three structures (Classes 1 and 3) were found to have structural properties typical for other stator complexes. In contrast, in Class 2 structures, the pentamer ring of the A subunits forms a C-shape, with lauryl maltose neopentyl glycol (LMNG) bound to the periplasmic side of the interface between the A and B subunits. This interface is conserved in all stator complexes, suggesting that hydrophobic ligands and lipids can bind to this interface, a feature that could potentially be utilized in the development of novel antibiotics aimed at regulating cell motility and infection.
External linksBiomolecules / PubMed:40149971 / PubMed Central
MethodsEM (single particle)
Resolution3.3 - 3.5 Å
Structure data

EMDB-63392, PDB-9lu9:
The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 1
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-63393, PDB-9lub:
The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 2
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-63394, PDB-9luc:
The chimeric flagellar motor complex between MotA1B1 from Paenibacillus sp. TCA20 and MotAB from E.coli, state 3
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

Source
  • paenibacillus sp. tca20 (bacteria)
  • escherichia coli (E. coli)
KeywordsMOTOR PROTEIN / Flagellar / motility / Paenibacillus

+
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