7ACY | pdb_00007acy

H/L (SLPH/SLPL) complex from C. difficile (CD630 strain)

• PDB DOI: https://doi.org/10.2210/pdb7ACY/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Clostridioides difficile 630
• Mutation(s): No 


• Deposited: 2020-09-11 Released: 2022-03-09 
• Deposition Author(s): Lanzoni-Mangutchi, P., Barwinska-Sendra, A., Salgado, P.S.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Models: experimental

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

• PubMed: 35217634 
• DOI: https://doi.org/10.1038/s41467-022-28196-w
• Primary Citation 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.

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Organizational Affiliation: 
• Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
Krebs Institute, School of Biosciences, University of Sheffield, Sheffield, UK.
Royal Society of Chemistry, Burlington House, Piccadilly, London, UK.
Florey Institute, School of Biosciences, University of Sheffield, Sheffield, UK.
Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
Department of Immunology, Oslo University Hospital, Oslo, Norway.
Diamond Light Source, Oxfordshire, UK.
Department of Life Sciences, Imperial College London, London, UK.
Krebs Institute, School of Biosciences, University of Sheffield, Sheffield, UK. [e-mail].
Krebs Institute, School of Biosciences, University of Sheffield, Sheffield, UK. [e-mail].
Florey Institute, School of Biosciences, University of Sheffield, Sheffield, UK. [e-mail].
Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 147.18 kDa 
• Atom Count: 10,418 
• Modeled Residue Count: 1,382 
• Deposited Residue Count: 1,382 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-layer protein	A, C	318	Clostridioides difficile 630	Mutation(s): 0
UniProt
Find proteins for Q183M8 (Clostridioides difficile (strain 630)) Explore Q183M8  Go to UniProtKB:  Q183M8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-layer protein	B, D	373	Clostridioides difficile 630	Mutation(s): 0
UniProt
Find proteins for Q183M8 (Clostridioides difficile (strain 630)) Explore Q183M8  Go to UniProtKB:  Q183M8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.67	α = 81.89
b = 78.25	β = 66.98
c = 81.58	γ = 65.26

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): Lanzoni-Mangutchi, P., Barwinska-Sendra, A., Salgado, P.S.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	204877/Z/16/Z

Revision History  

• Version 1.0: 2022-03-09
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description