[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

TitleHexameric and pentameric complexes of the ExbBD energizer in the Ton system.
Journal, issue, pagesElife, Vol. 7, Year 2018
Publish dateApr 17, 2018
AuthorsSaori Maki-Yonekura / Rei Matsuoka / Yoshiki Yamashita / Hirofumi Shimizu / Maiko Tanaka / Fumie Iwabuki / Koji Yonekura /
PubMed AbstractGram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three ...Gram-negative bacteria import essential nutrients such as iron and vitamin B through outer membrane receptors. This process utilizes proton motive force harvested by the Ton system made up of three inner membrane proteins, ExbB, ExbD and TonB. ExbB and ExbD form the proton channel that energizes uptake through TonB. Recently, crystal structures suggest that the ExbB pentamer is the scaffold. Here, we present structures of hexameric complexes of ExbB and ExbD revealed by X-ray crystallography and single particle cryo-EM. Image analysis shows that hexameric and pentameric complexes coexist, with the proportion of hexamer increasing with pH. Channel current measurement and 2D crystallography support the existence and transition of the two oligomeric states in membranes. The hexameric complex consists of six ExbB subunits and three ExbD transmembrane helices enclosed within the central channel. We propose models for activation/inactivation associated with hexamer and pentamer formation and utilization of proton motive force.
External linksElife / PubMed:29661272 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.84 - 7.1 Å
Structure data

EMDB-6927, PDB-5zfu:
Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
Method: EM (single particle) / Resolution: 6.7 Å

EMDB-6928, PDB-5zfv:
Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)
Method: EM (single particle) / Resolution: 7.1 Å

PDB-5zfp:
Structure of the ExbB/ExbD hexameric complex
Method: X-RAY DIFFRACTION / Resolution: 2.84 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • Escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
KeywordsTRANSPORT PROTEIN / TON SYSTEM / ION CHANNEL / ENERGIZER / TRANSPORTER / PROTON MOTIVE FORCE

+
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