7ACX

H/L (SLPH/SLPL) complex from C. difficile (R7404 strain)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


This is version 1.1 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
317Clostridioides difficileMutation(s): 0 
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
373Clostridioides difficileMutation(s): 0 
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: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.052α = 90
b = 137.94β = 100.7
c = 84.734γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description