6UWT

Clostridium difficile binary toxin translocase CDTb tetradecamer in symmetric conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Structure of the cell-binding component of theClostridium difficilebinary toxin reveals a di-heptamer macromolecular assembly.

Xu, X.Godoy-Ruiz, R.Adipietro, K.A.Peralta, C.Ben-Hail, D.Varney, K.M.Cook, M.E.Roth, B.M.Wilder, P.T.Cleveland, T.Grishaev, A.Neu, H.M.Michel, S.L.J.Yu, W.Beckett, D.Rustandi, R.R.Lancaster, C.Loughney, J.W.Kristopeit, A.Christanti, S.Olson, J.W.MacKerell, A.D.Georges, A.D.Pozharski, E.Weber, D.J.

(2020) Proc Natl Acad Sci U S A 117: 1049-1058

  • DOI: https://doi.org/10.1073/pnas.1919490117
  • Primary Citation of Related Structures:  
    6UWI, 6UWO, 6UWR, 6UWT

  • PubMed Abstract: 

    Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single-particle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including a symmetric ( Sym CDTb; 3.14 Å) and an asymmetric form ( Asym CDTb; 2.84 Å). Roles played by 2 receptor-binding domains of activated CDTb were of particular interest since the receptor-binding domain 1 lacks sequence homology to any other known toxin, and the receptor-binding domain 2 is completely absent in other well-studied heptameric toxins (i.e., anthrax). For Asym CDTb, a Ca 2+ binding site was discovered in the first receptor-binding domain that is important for its stability, and the second receptor-binding domain was found to be critical for host cell toxicity and the di-heptamer fold for both forms of activated CDTb. Together, these studies represent a starting point for developing structure-based drug-design strategies to target the most severe strains of C. difficile .


  • Organizational Affiliation

    City University of New York Advanced Science Research Center, City University of New York, New York, NY 10017.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyltransferase binding component667Clostridioides difficileMutation(s): 0 
Gene Names: cdtB
Membrane Entity: Yes 
UniProt
Find proteins for O32739 (Clostridioides difficile)
Explore O32739 
Go to UniProtKB:  O32739
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32739
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 
AA [auth N]
BA [auth N]
CA [auth A]
DA [auth A]
EA [auth B]
AA [auth N],
BA [auth N],
CA [auth A],
DA [auth A],
EA [auth B],
FA [auth B],
GA [auth C],
HA [auth C],
IA [auth D],
JA [auth D],
KA [auth E],
LA [auth E],
MA [auth F],
NA [auth F],
O [auth H],
OA [auth G],
P [auth H],
PA [auth G],
Q [auth I],
R [auth I],
S [auth J],
T [auth J],
U [auth K],
V [auth K],
W [auth L],
X [auth L],
Y [auth M],
Z [auth M]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations