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 

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:  
    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 p ...

    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
Find similar proteins by:  (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
Find proteins for Q18A65 (Clostridioides difficile (strain 630))
Explore Q18A65 
Go to UniProtKB:  Q18A65
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

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

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TYRKd:  94000   nM  Binding MOAD
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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