6OKU

CDTb Double Heptamer Long Form Mask 3 Modeled from Cryo-EM Map Reconstructed using C7 Symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the transition of Clostridioides difficile binary toxin from prepore to pore.

Anderson, D.M.Sheedlo, M.J.Jensen, J.L.Lacy, D.B.

(2020) Nat Microbiol 5: 102-107

  • DOI: https://doi.org/10.1038/s41564-019-0601-8
  • Primary Citation of Related Structures:  
    6O2M, 6O2N, 6O2O, 6OKR, 6OKS, 6OKT, 6OKU

  • PubMed Abstract: 

    Clostridioides (formerly Clostridium) difficile is a Gram-positive, spore-forming anaerobe and a leading cause of hospital-acquired infection and gastroenteritis-associated death in US hospitals 1 . The disease state is usually preceded by disruption of the host microbiome in response to antibiotic treatment and is characterized by mild to severe diarrhoea. C. difficile infection is dependent on the secretion of one or more AB-type toxins: toxin A (TcdA), toxin B (TcdB) and the C. difficile transferase toxin (CDT) 2 . Whereas TcdA and TcdB are considered the primary virulence factors, recent studies suggest that CDT increases the severity of C. difficile infection in some of the most problematic clinical strains 3 . To better understand how CDT functions, we used cryo-electron microscopy to define the structure of CDTb, the cell-binding component of CDT. We obtained structures of several oligomeric forms that highlight the conformational changes that enable conversion from a prepore to a β-barrel pore. The structural analysis also reveals a glycan-binding domain and residues involved in binding the host-cell receptor, lipolysis-stimulated lipoprotein receptor. Together, these results provide a framework to understand how CDT functions at the host cell interface.


  • Organizational Affiliation

    Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyltransferase binding component
A, B, C, D, E
A, B, C, D, E, F, G
876Clostridioides difficileMutation(s): 0 
Gene Names: cdtB
Membrane Entity: Yes 
UniProt
Find proteins for A8DS70 (Clostridioides difficile)
Explore A8DS70 
Go to UniProtKB:  A8DS70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8DS70
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited StatesBX002943
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI095755

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.2: 2020-05-13
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references