The ligand-bound, open structure of CD0873, a substrate binding protein with adhesive properties from Clostridium difficile.

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Molecular features of lipoprotein CD0873: A potential vaccine against the human pathogenClostridioides difficile.

Bradshaw, W.J.Bruxelle, J.F.Kovacs-Simon, A.Harmer, N.J.Janoir, C.Pechine, S.Acharya, K.R.Michell, S.L.

(2019) J Biol Chem 294: 15850-15861

  • DOI: https://doi.org/10.1074/jbc.RA119.010120
  • Primary Citation of Related Structures:  
    6HNI, 6HNJ, 6HNK

  • PubMed Abstract: 

    Clostridioides difficile is the primary cause of antibiotic-associated diarrhea and colitis, a healthcare-associated intestinal disease resulting in a significant fatality rate. Colonization of the gut is critical for C. difficile pathogenesis. The bacterial molecules essential for efficient colonization therefore offer great potential as vaccine candidates. Here we present findings demonstrating that the C. difficile immunogenic lipoprotein CD0873 plays a critical role in pathogen success in vivo We found that in a dixenic colonization model, a CD0873-positive strain of C. difficile significantly outcompeted a CD0873-negative strain. Immunization of mice with recombinant CD0873 prevented long-term gut colonization and was correlated with a strong secretory IgA immune response. We further present high-resolution crystal structures of CD0873, at 1.35-2.50 Å resolutions, offering a first view of the ligand-binding pocket of CD0873 and provide evidence that this lipoprotein adhesin is part of a tyrosine import system, an amino acid key in C. difficile infection. These findings suggest that CD0873 could serve as an effective component in a vaccine against C. difficile .

  • Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-type transport system, sugar-family extracellular solute-binding protein319Clostridioides difficile 630Mutation(s): 1 
Gene Names: CD630_08730
Find proteins for Q18A65 (Clostridioides difficile (strain 630))
Explore Q18A65 
Go to UniProtKB:  Q18A65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18A65
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PGE

Download Ideal Coordinates CCD File 
C6 H14 O4
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.963α = 90
b = 57.534β = 90
c = 148.526γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references