6HNI

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

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Literature

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

  • 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 ...

    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: 

    College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom S.L.Michell@exeter.ac.uk.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC-type transport system, sugar-family extracellular solute-binding proteinA319Clostridioides difficile 630Mutation(s): 1 
Gene Names: CD630_08730
UniProt
Find proteins for Q18A65 (Clostridioides difficile (strain 630))
Explore Q18A65 
Go to UniProtKB:  Q18A65
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
TYR Binding MOAD:  6HNI Kd: 9.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.107α = 90
b = 42.351β = 94.76
c = 56.175γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

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