6V1S

Structure of the Clostridioides difficile transferase toxin


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 1.2 of the entry. See complete history


Literature

Structural elucidation of theClostridioides difficiletransferase toxin reveals a single-site binding mode for the enzyme.

Sheedlo, M.J.Anderson, D.M.Thomas, A.K.Lacy, D.B.

(2020) Proc Natl Acad Sci U S A 117: 6139-6144

  • DOI: https://doi.org/10.1073/pnas.1920555117
  • Primary Citation of Related Structures:  
    6V1S

  • PubMed Abstract: 

    Clostridioides difficile is a Gram-positive, pathogenic bacterium and a prominent cause of hospital-acquired diarrhea in the United States. The symptoms of C. difficile infection are caused by the activity of three large toxins known as toxin A (TcdA), toxin B (TcdB), and the C. difficile transferase toxin (CDT). Reported here is a 3.8-Å cryo-electron microscopy (cryo-EM) structure of CDT, a bipartite toxin comprised of the proteins CDTa and CDTb. We observe a single molecule of CDTa bound to a CDTb heptamer. The formation of the CDT complex relies on the interaction of an N-terminal adaptor and pseudoenzyme domain of CDTa with six subunits of the CDTb heptamer. CDTb is observed in a preinsertion state, a conformation observed in the transition of prepore to β-barrel pore, although we also observe a single bound CDTa in the prepore and β-barrel conformations of CDTb. The binding interaction appears to prime CDTa for translocation as the adaptor subdomain enters the lumen of the preinsertion state channel. These structural observations advance the understanding of how a single protein, CDTb, can mediate the delivery of a large enzyme, CDTa, into the cytosol of mammalian cells.


  • Organizational Affiliation

    Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232.


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
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylating binary toxin enzymatic subunit CdtAH [auth Z]463Clostridioides difficileMutation(s): 0 
Gene Names: cdtAE5N70_18065SAMEA897066_00723
EC: 2.4.2
UniProt
Find proteins for Q9KH42 (Clostridioides difficile)
Explore Q9KH42 
Go to UniProtKB:  Q9KH42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KH42
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 
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

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 StatesAI095755
Other governmentUnited StatesBX002943

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations