[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

TitleOligomerization of the Clostridioides difficile transferase B component proceeds through a stepwise mechanism.
Journal, issue, pagesPLoS Pathog, Vol. 21, Issue 7, Page e1013186, Year 2025
Publish dateJul 21, 2025
AuthorsRobin M Mullard / Michael J Sheedlo /
PubMed AbstractClostridioides difficile is a gram-positive, pathogenic bacterium and is currently the leading cause of hospital-acquired, infectious diarrhea in the United States. During infection, C. difficile ...Clostridioides difficile is a gram-positive, pathogenic bacterium and is currently the leading cause of hospital-acquired, infectious diarrhea in the United States. During infection, C. difficile produces and secretes up to three toxins called Toxin A, Toxin B, and the C. difficile transferase (CDT). While Toxin A and Toxin B are thought to drive the pathology associated with the disease, strains that produce CDT have been linked to increased disease severity, higher rates of infection recurrence, and increased incidence of mortality. A basic understanding of how CDT intoxicates host cells has emerged over the past two decades and includes a framework that relies on the oligomerization of the components that comprise CDT to promote cellular intoxication. Although several key steps of this process have been biochemically described, a clear, molecular description of toxin assembly has not been resolved. We have collected cryogenic electron microscopy (Cryo-EM) data of purified, recombinant CDT. From these data, we have generated several structural snapshots of the toxin, including a series of structures that correspond to intermediates that form during oligomerization. These structures provide insight into the mechanism underlying toxin assembly and highlight a role for structural plasticity during this process. We have also shown that these partially assembled toxins are equally potent in cytotoxicity assays supporting this model in a cellular context. Finally, we show that CDTb oligomers are stabilized by CDTa and assembly is triggered by hydrophobic molecules.
External linksPLoS Pathog / PubMed:40690518 / PubMed Central
MethodsEM (single particle)
Resolution3.33 - 12.05 Å
Structure data

EMDB-48170: Low Resolution Cryo-EM Map of the Clostridioides difficile Transferase Component B Monomer
Method: EM (single particle) / Resolution: 6.97 Å

EMDB-48171, PDB-9mdi:
Clostridioides difficile Transferase B Component Dimer
Method: EM (single particle) / Resolution: 3.56 Å

EMDB-48172, PDB-9mdj:
Clostridioides difficile Transferase B Component Dimer in Complex with the A Component
Method: EM (single particle) / Resolution: 5.17 Å

EMDB-48173, PDB-9mdl:
Clostridioides difficile Transferase B Component Trimer
Method: EM (single particle) / Resolution: 4.19 Å

EMDB-48174, PDB-9mdn:
Clostridioides difficile Transferase B Component Trimer in Complex with the A Component
Method: EM (single particle) / Resolution: 7.86 Å

EMDB-48175, PDB-9mdp:
Clostridioides difficile Transferase B Component Tetramer
Method: EM (single particle) / Resolution: 7.01 Å

EMDB-48176: Clostridioides difficile Transferase B Component Pentamer
Method: EM (single particle) / Resolution: 10.32 Å

EMDB-48177: Clostridioides difficile Transferase B Component Hexamer
Method: EM (single particle) / Resolution: 12.05 Å

EMDB-48178, PDB-9mdr:
Clostridioides difficile Transferase B Component Symmetric Heptamer
Method: EM (single particle) / Resolution: 3.33 Å

Chemicals

ChemComp-CA:
Unknown entry

Source
  • clostridioides difficile r20291 (bacteria)
KeywordsTOXIN / Clostridioides / Iota / ADP-ribosyltransferase

+
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