7ACW

LID/HID (LMW SLP and HMW SLP interacting domains) from C. difficile (R7404 strain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure and assembly of the S-layer in C. difficile.

Lanzoni-Mangutchi, P.Banerji, O.Wilson, J.Barwinska-Sendra, A.Kirk, J.A.Vaz, F.O'Beirne, S.Basle, A.El Omari, K.Wagner, A.Fairweather, N.F.Douce, G.R.Bullough, P.A.Fagan, R.P.Salgado, P.S.

(2022) Nat Commun 13: 970-970

  • DOI: https://doi.org/10.1038/s41467-022-28196-w
  • Primary Citation of Related Structures:  
    7ACV, 7ACW, 7ACX, 7ACY, 7ACZ, 7QGQ

  • PubMed Abstract: 

    Many bacteria and archaea possess a two-dimensional protein array, or S-layer, that covers the cell surface and plays crucial roles in cell physiology. Here, we report the crystal structure of SlpA, the main S-layer protein of the bacterial pathogen Clostridioides difficile, and use electron microscopy to study S-layer organisation and assembly. The SlpA crystal lattice mimics S-layer assembly in the cell, through tiling of triangular prisms above the cell wall, interlocked by distinct ridges facing the environment. Strikingly, the array is very compact, with pores of only ~10 Å in diameter, compared to other S-layers (30-100 Å). The surface-exposed flexible ridges are partially dispensable for overall structure and assembly, although a mutant lacking this region becomes susceptible to lysozyme, an important molecule in host defence. Thus, our work gives insights into S-layer organisation and provides a basis for development of C. difficile-specific therapeutics.


  • Organizational Affiliation

    Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-layer protein
A, C
78Clostridioides difficileMutation(s): 0 
Gene Names: slpASAMEA708418_00075
EC: 3.5.1.28
UniProt
Find proteins for Q9AEM2 (Clostridioides difficile)
Explore Q9AEM2 
Go to UniProtKB:  Q9AEM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AEM2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S-layer protein
B, D
50Clostridioides difficileMutation(s): 0 
Gene Names: slpASAMEA708418_00075
EC: 3.5.1.28
UniProt
Find proteins for Q9AEM2 (Clostridioides difficile)
Explore Q9AEM2 
Go to UniProtKB:  Q9AEM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AEM2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.273α = 90
b = 56.705β = 122.71
c = 61.813γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204877/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release