3CVZ | pdb_00003cvz

Structural insights into the molecular organization of the S-layer from Clostridium difficile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.294 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural insights into the molecular organization of the S-layer from Clostridium difficile

Fagan, R.P.Albesa-Jove, D.Qazi, O.Svergun, D.I.Brown, K.A.Fairweather, N.F.

(2009) Mol Microbiol 71: 1308-1322

  • DOI: https://doi.org/10.1111/j.1365-2958.2009.06603.x
  • Primary Citation Related Structures: 
    3CVZ

  • PubMed Abstract: 

    Clostridium difficile expresses a surface layer (S-layer) which coats the surface of the bacterium and acts as an adhesin facilitating interaction of the bacterium with host enteric cells. The S-layer contains a high-molecular-weight S-layer protein (HMW SLP) and its low-molecular-weight partner protein (LMW SLP). We show that these proteins form a tightly associated non-covalent complex, the H/L complex, and we identify the regions of both proteins responsible for complex formation. The 2.4 A X-ray crystal structure of a truncated derivative of the LMW SLP reveals two domains. Domain 1 has a two-layer sandwich architecture while domain 2, predicted to orientate towards the external environment, contains a novel fold. Small-angle X-ray scattering analysis of the H/L complex shows an elongated molecule, with the two SLPs arranged 'end-to-end' interacting with each other through a small contact area. Alignment of LMW SLPs, which exhibit high sequence diversity, reveals a core of conserved residues that could reflect functional conservation, while allowing for immune evasion through sequence variation. These structures are the first described for the S-layer of a bacterial pathogen, and provide insights into the assembly and biogenesis of the S-layer.


  • Organizational Affiliation
    • Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW72AZ, UK.

Macromolecule Content 

  • Total Structure Weight: 116.49 kDa 
  • Atom Count: 7,641 
  • Modeled Residue Count: 976 
  • Deposited Residue Count: 1,092 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-layer protein
A, B, C, D
273Clostridioides difficileMutation(s): 0 
Gene Names: slpA
UniProt
Find proteins for Q183M8 (Clostridioides difficile (strain 630))
Explore Q183M8 
Go to UniProtKB:  Q183M8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ183M8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.294 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.059α = 90
b = 107.059β = 90
c = 190.617γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations