2F6E | pdb_00002f6e

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2F6E

This is version 1.4 of the entry. See complete history

Literature

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 Related Structures: 
    2F6E

  • 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.

Macromolecule Content 

  • Total Structure Weight: 14.2 kDa 
  • Atom Count: 1,155 
  • Modeled Residue Count: 125 
  • Deposited Residue Count: 127 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toxin A127Clostridioides difficileMutation(s): 6 
Gene Names: toxAtcdA
EC: 3.4.22
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
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
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



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