9MDP | pdb_00009mdp

Clostridioides difficile Transferase B Component Tetramer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Oligomerization of the Clostridioides difficile transferase B component proceeds through a stepwise mechanism.

Mullard, R.M.Sheedlo, M.J.

(2025) PLoS Pathog 21: e1013186-e1013186

  • DOI: https://doi.org/10.1371/journal.ppat.1013186
  • Primary Citation of Related Structures:  
    9MDI, 9MDJ, 9MDL, 9MDN, 9MDP, 9MDR

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, Minnesota, United States of America.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adp-ribosyltransferase binding component
A, B, C, D
876Clostridioides difficile R20291Mutation(s): 0 
Gene Names: CDR20291_2492
UniProt
Find proteins for A0A9R0BM17 (Clostridioides difficile (strain R20291))
Explore A0A9R0BM17 
Go to UniProtKB:  A0A9R0BM17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9R0BM17
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR00AI154672

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references