Clostridioides difficile R20291 minor pilin - PilW fused with Maltose Binding Protein

Experimental Data Snapshot

  • Resolution: 2.49 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7T31


Recognition of extracellular DNA by type IV pili promotes biofilm formation by Clostridioides difficile.

Ronish, L.A.Sidner, B.Yu, Y.Piepenbrink, K.H.

(2022) J Biol Chem 298: 102449-102449

  • DOI: https://doi.org/10.1016/j.jbc.2022.102449
  • Primary Citation of Related Structures:  
    7T31, 8DX4

  • PubMed Abstract: 

    Clostridioides difficile is a Gram-positive bacillus, which is a frequent cause of gastrointestinal infections triggered by the depletion of the gut microbiome. Because of the frequent recurrence of these infections after antibiotic treatment, mechanisms of C. difficile persistence and recurrence, including biofilm formation, are of increasing interest. Previously, our group and others found that type IV pili, filamentous helical appendages polymerized from protein subunits, promoted microcolony and biofilm formation in C. difficile. In Gram-negative bacteria, the ability of type IV pili to mediate bacterial self-association has been explained through interactions between the pili of adjacent cells, but type IV pili from several Gram-negative species are also required for natural competence through DNA uptake. Here, we report the ability of two C. difficile pilin subunits, PilJ and PilW, to bind to DNA in vitro, as well as the defects in biofilm formation in the pilJ and pilW gene-interruption mutants. Additionally, we have resolved the X-ray crystal structure of PilW, which we use to model possible structural mechanisms for the formation of C. difficile biofilm through interactions between type IV pili and the DNA of the extracellular matrix. Taken together, our results provide further insight into the relationship between type IV pilus function and biofilm formation in C. difficile and, more broadly, suggest that DNA recognition by type IV pili and related structures may have functional importance beyond DNA uptake for natural competence.

  • Organizational Affiliation

    Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Putative pilin protein
A, B, C, D
512Escherichia coliClostridioides difficile R20291
This entity is chimeric
Mutation(s): 0 
Gene Names: malEJW3994CD196_2148
Find proteins for A0A0H3N4W9 (Clostridioides difficile (strain CD196))
Explore A0A0H3N4W9 
Go to UniProtKB:  A0A0H3N4W9
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0H3N4W9P0AEX9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EPE

Download Ideal Coordinates CCD File 
C8 H18 N2 O4 S
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 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
P [auth C],
Q [auth D],
S [auth D],
T [auth D],
U [auth D],
W [auth D],
X [auth D],
Y [auth D]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.49 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.326α = 92.44
b = 81.796β = 90.95
c = 102.964γ = 113.37
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoXDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesK22 AI123467
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP20-GM113126

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description