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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • PubMed Abstract: 
  • <i>Clostridioides difficile </i> is the primary cause of antibiotic-associated diarrhoea and colitis, a healthcare-associated intestinal disease resulting in a significant fatality rate. Colonization of the gut is critical for <i>C. difficile </i> ...

    Clostridioides difficile is the primary cause of antibiotic-associated diarrhoea and colitis, a healthcare-associated intestinal disease resulting in a significant fatality rate. Colonization of the gut is critical for C. difficile pathogenesis, and 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 1.80-2.50 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 a effective component in a vaccine against C. difficile .


    Organizational Affiliation

    University of Exeter, United Kingdom.,University of Bath, United Kingdom.,University of Exeter.,Structural Genomics Consortium, University of Oxford, United Kingdom.,Université Paris-Saclay, France.,Université Paris-Sud, Université Paris-Saclay, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC-type transport system, sugar-family extracellular solute-binding protein
A
319Clostridioides difficile (strain 630)Mutation(s): 1 
Find proteins for Q18A65 (Clostridioides difficile (strain 630))
Go to UniProtKB:  Q18A65
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download SDF File 
Download CCD File 
A
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.107α = 90.00
b = 42.351β = 94.76
c = 56.175γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Database references