4DXG

Crystal structure of Staphylococcal Superantigen-Like protein 4 complexed with sialyl Lewis X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and functional properties of staphylococcal superantigen-like protein 4

Hermans, S.J.Baker, H.M.Sequeira, R.P.Langley, R.J.Baker, E.N.Fraser, J.D.

(2012) Infect.Immun. 80: 4004-4013

  • DOI: 10.1128/IAI.00764-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Staphylococcus aureus is a prevalent and significant human pathogen. Among the repertoire of virulence factors produced by this bacterium are the 14 staphylococcal superantigen-like (SSL) proteins. SSL protein 4 (SSL4) is one member of this family an ...

    Staphylococcus aureus is a prevalent and significant human pathogen. Among the repertoire of virulence factors produced by this bacterium are the 14 staphylococcal superantigen-like (SSL) proteins. SSL protein 4 (SSL4) is one member of this family and contains a highly conserved carbohydrate binding site also found in SSL2, SSL3, SSL5, SSL6, and SSL11. Recombinant SSL4(t), comprising amino acids 109 to 309 of Newman strain SSL4 (SSL4-Newman), has been shown to bind and be internalized by human granulocytes and macrophages in a sialic-acid (Sia)-dependent manner. SSL4(t) can compete with itself for cell binding, indicating that binding is target specific. A 2.5-Å-resolution crystal structure of SSL4(t) complexed with sialyl Lewis X (sLe(x)) [sLe(x)-Neu5Acα2-3Galβ1-4(Fucα1-3)GlcNAc] revealed a similar binding site to SSL5 and SSL11. These data, along with data on SSL4(t) binding to a glycan array and biosensor analysis of sLe(x) and sialyllactosamine (sLacNac) binding are compared with those for SSL11. Although these proteins show great similarity in their carbohydrate binding sites, with a root mean square (RMS) difference between main chain atom positions of only 0.34 Å, these proteins differ in detail in their affinity for sLe(x) and sLacNac, as well as their glycan preference. Together with cell binding data, this shows how S. aureus produces multiple related proteins that target myeloid cells through specific sialyllactosamine-containing glycoproteins.


    Organizational Affiliation

    School of Medical Sciences, University of Auckland, Aukland, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Staphylococcal enterotoxin-like toxin
A
204Staphylococcus aureus (strain Newman)Mutation(s): 0 
Gene Names: ssl4
Find proteins for A0A0H3K6A3 (Staphylococcus aureus (strain Newman))
Go to UniProtKB:  A0A0H3K6A3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIN
Query on PIN

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Download CCD File 
A
PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
PIPES; 1,4-PIPERAZINEDIETHANESULFONIC ACID
C8 H18 N2 O6 S2
IHPYMWDTONKSCO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.185 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.880α = 90.00
b = 78.880β = 90.00
c = 97.701γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
MAR345dtbdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references