6CWL

Crystal structure of SpaA-SLH in complex with beta-D-GlcNAc-(1->3)-4,6-Pyr-beta-D-ManNAcOMe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei.

Blackler, R.J.Lopez-Guzman, A.Hager, F.F.Janesch, B.Martinz, G.Gagnon, S.M.L.Haji-Ghassemi, O.Kosma, P.Messner, P.Schaffer, C.Evans, S.V.

(2018) Nat Commun 9: 3120-3120

  • DOI: https://doi.org/10.1038/s41467-018-05471-3
  • Primary Citation of Related Structures:  
    6CWC, 6CWF, 6CWH, 6CWI, 6CWL, 6CWM, 6CWN, 6CWR

  • PubMed Abstract: 

    Self-assembling protein surface (S-) layers are common cell envelope structures of prokaryotes and have critical roles from structural maintenance to virulence. S-layers of Gram-positive bacteria are often attached through the interaction of S-layer homology (SLH) domain trimers with peptidoglycan-linked secondary cell wall polymers (SCWPs). Here we present an in-depth characterization of this interaction, with co-crystal structures of the three consecutive SLH domains from the Paenibacillus alvei S-layer protein SpaA with defined SCWP ligands. The most highly conserved SLH domain residue SLH-Gly29 is shown to enable a peptide backbone flip essential for SCWP binding in both biophysical and cellular experiments. Furthermore, we find that a significant domain movement mediates binding by two different sites in the SLH domain trimer, which may allow anchoring readjustment to relieve S-layer strain caused by cell growth and division.


  • Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Surface (S-) layer glycoprotein
A, B
182Paenibacillus alveiMutation(s): 0 
Gene Names: spaA
UniProt
Find proteins for C1JZ07 (Paenibacillus alvei)
Explore C1JZ07 
Go to UniProtKB:  C1JZ07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1JZ07
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FHY
Query on FHY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S,4aR,6R,7S,8R,8aS)-7-(acetylamino)-6-({2-(acetylamino)-3-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-4,6-O-[(1S)-1-carboxylic acidethylidene]-2-deoxy-beta-D-mannopyranosyl}oxy)-8-{[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]oxy}-2-methylhexahydro-2H-pyrano[3,2-d][1,3]dioxine-2-carboxylic acid
C20 H32 N2 O13
HMXWDMHKOICGNH-MYXXRMNRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.256α = 90
b = 72.256β = 90
c = 126.14γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaCGSD3-426678-2012
Austrian Science FundAustriaP22791-B12
Austrian Science FundAustriaP27374-B22

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description