1M4V | pdb_00001m4v

Crystal structure of SET3, a superantigen-like protein from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1M4V

This is version 1.3 of the entry. See complete history

Literature

The three-dimensional structure of a superantigen-like protein, SET3, from a pathogenicity island of the Staphylococcus aureus genome

Arcus, V.L.Langley, R.Proft, T.Fraser, J.D.Baker, E.N.

(2002) J Biological Chem 277: 32274-32281

  • DOI: https://doi.org/10.1074/jbc.M203914200
  • Primary Citation Related Structures: 
    1M4V

  • PubMed Abstract: 

    The staphylococcal enterotoxin-like toxins (SETs) are a family of proteins encoded within the Staphylococcus aureus genome that were identified by their similarity to the well described bacterial superantigens. The first crystal structure of a member of the SET family, SET3, has been determined to 1.9 A (R = 0.205, R(free) = 0.240) and reveals a fold characteristic of the superantigen family but with significant differences. The SET proteins are secreted at varying levels by staphylococcal isolates, and seroconversion studies of normal individuals indicate that they are strongly antigenic to humans. Recombinant SETs do not exhibit any of the properties expected of superantigens such as major histocompatibility complex class II binding or broad T-cell activation, suggesting they have an entirely different function. The fact that the whole gene family is clustered within the pathogenicity island SaIn2 of the S. aureus genome suggests that they are involved in host/pathogen interactions.


  • Organizational Affiliation
    • School of Biological Sciences, University of Auckland, Private Bag 92-019 Auckland, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 48.43 kDa 
  • Atom Count: 3,677 
  • Modeled Residue Count: 393 
  • Deposited Residue Count: 408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SET3, superantigen-like protein
A, B
204Staphylococcus aureusMutation(s): 0 
Gene Names: SET3
UniProt
Find proteins for Q9ZFS6 (Staphylococcus aureus)
Explore Q9ZFS6 
Go to UniProtKB:  Q9ZFS6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZFS6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.123α = 90
b = 65.123β = 90
c = 196.731γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references