[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 diversity and oligomerization of bacterial ubiquitin-like proteins.
Journal, issue, pagesStructure, Vol. 33, Issue 6, Page 1016-11026.e4, Year 2025
Publish dateJun 5, 2025
AuthorsMinheng Gong / Qiaozhen Ye / Yajie Gu / Lydia R Chambers / Andrey A Bobkov / Neal K Arakawa / Mariusz Matyszewski / Kevin D Corbett /
PubMed AbstractBacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have ...Bacteria possess a variety of operons with homology to eukaryotic ubiquitination pathways that encode predicted E1, E2, E3, deubiquitinase, and ubiquitin-like proteins. Some of these pathways have recently been shown to function in anti-bacteriophage immunity, but the biological functions of others remain unknown. Here, we show that ubiquitin-like proteins in two bacterial operon families show surprising architectural diversity, possessing one to three β-grasp domains preceded by diverse N-terminal domains. We find that a large group of bacterial ubiquitin-like proteins possess three β-grasp domains and form homodimers and helical filaments mediated by conserved Ca ion binding sites. Our findings highlight a distinctive mode of self-assembly for ubiquitin-like proteins and suggest that Ca-mediated ubiquitin-like protein filament assembly and/or disassembly enables cells to sense and respond to stress conditions that alter intracellular metal ion concentration.
External linksStructure / PubMed:40250427 / PubMed Central
MethodsEM (helical sym.) / EM (single particle) / X-ray diffraction
Resolution1.87 - 3.08 Å
Structure data

46576

9d59

EMDB-46576, PDB-9d59:
Structure of Citrobacter multi-ubiquitin protein filament
Method: EM (helical sym.) / Resolution: 2.43 Å

46577

9d5a

EMDB-46577, PDB-9d5a:
Structure of Citrobacter multi-ubiquitin protein, local refinement of one full-length protomer
Method: EM (single particle) / Resolution: 2.73 Å

46578

9d5b

EMDB-46578, PDB-9d5b:
Structure of Methylobacterium brachiatum multi-ubiquitin protein filament
Method: EM (helical sym.) / Resolution: 3.08 Å

PDB-8u38:
Structure of a bacterial multi-ubiquitin domain protein
Method: X-RAY DIFFRACTION / Resolution: 3.04 Å

PDB-9cd2:
Structure of E. coli ZDHYS365 multi-ubiquitin domain protein
Method: X-RAY DIFFRACTION / Resolution: 1.87 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

Source
  • citrobacter sp. rhbstw-00271 (bacteria)
  • methylobacterium brachiatum (bacteria)
  • escherichia coli (E. coli)
KeywordsPROTEIN BINDING / antiviral / anti-phage / ubiquitin / filament / beta-grasp

+
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