6UWR

Clostridium difficile binary toxin translocase CDTb in asymmetric tetradecamer conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.USA 117: 1049-1058

  • DOI: 10.1073/pnas.1919490117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting <i>Clostridium difficile </i> infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent <i>C. difficile </i> strains often have a binary toxin termed th ...

    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

    Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742.,PhD Program in Biochemistry, The Graduate Center, City University of New York, New York, NY 10017.,PhD Program in Chemistry, The Graduate Center, City University of New York, New York, NY 10017.,Department of Chemistry & Biochemistry, City College of New York, New York, NY 10031.,The Center for Biomolecular Therapeutics, The University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201.,National Institute of Standards, Rockville, MD 20899.,City University of New York Advanced Science Research Center, City University of New York, New York, NY 10017; adesgeorges@gc.cuny.edu EPozharskiy@som.umaryland.edu dweber@som.umaryland.edu.,City University of New York Advanced Science Research Center, City University of New York, New York, NY 10017.,University of Maryland School of Pharmacy, University of Maryland, Baltimore, MD 21201.,Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201.,Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850.,Merck & Co., Inc., Kenilworth, NJ 07033.,Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, University of Maryland, Baltimore, MD 21201; adesgeorges@gc.cuny.edu EPozharskiy@som.umaryland.edu dweber@som.umaryland.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyltransferase binding component
A, B, C, D, E, F, G, H, I, J, K, L, M, N
667Clostridioides difficileMutation(s): 0 
Gene Names: cdtB
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
binary toxin translocase CDTb in asymmetric tetradecamer conformation
Find proteins for O32739 (Clostridioides difficile)
Go to UniProtKB:  O32739
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
phenix.real_space_refinerefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release