Clostridium difficile Toxin A C-terminal fragment 1 (TcdA-f1)

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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This is version 1.4 of the entry. See complete history


Crystal structure of receptor-binding C-terminal repeats from Clostridium difficile toxin A

Ho, J.G.Greco, A.Rupnik, M.Ng, K.K.

(2005) Proc Natl Acad Sci U S A 102: 18373-18378

  • DOI: https://doi.org/10.1073/pnas.0506391102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Clostridium difficile is a major nosocomial pathogen that produces two large protein toxins [toxin A (TcdA) and toxin B (TcdB)] capable of disrupting intestinal epithelial cells. Both belong to the family of large clostridial cytotoxins, which are characterized by the presence of a repetitive C-terminal repetitive domain (CRD). In TcdA, the CRD is composed of 39 repeats that are responsible for binding to cell surface carbohydrates. To understand the molecular structural basis of cell binding by the toxins from C. difficile, we have determined a 1.85-A resolution crystal structure of a 127-aa fragment from the C terminus of the toxin A CRD. This structure reveals a beta-solenoid fold containing five repeats, with each repeat consisting of a beta-hairpin followed by a loop of 7-10 residues in short repeats (SRs) or 18 residues in long repeats (LRs). Adjacent pairs of beta-hairpins are related to each other by either 90 degree or 120 degree screw-axis rotational relationships, depending on the nature of the amino acids at key positions in adjacent beta-hairpins. Models of the complete CRDs of toxins A and B suggest that each CRD contains straight stretches of beta-solenoid composed of three to five SRs that are punctuated by kinks introduced by the presence of a single LR. These structural features provide a framework for understanding how large clostridial cytotoxins bind to cell surfaces and suggest approaches for developing novel treatments for C. difficile-associated diseases by blocking the binding of toxins to cell surfaces.

  • Organizational Affiliation

    Alberta Ingenuity Centre for Carbohydrate Sciences, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin A127Clostridioides difficileMutation(s): 6 
Gene Names: toxAtcdA
Find proteins for P16154 (Clostridioides difficile)
Explore P16154 
Go to UniProtKB:  P16154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16154
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.05α = 90
b = 42.05β = 90
c = 132.11γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references
  • Version 1.4: 2024-05-29
    Changes: Data collection