2J4X

Streptococcus dysgalactiae-derived mitogen (SDM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Streptococcus Dysgalactiae-Derived Mitogen Reveals a Zinc-Binding Site and Alterations in Tcr Binding.

Saarinen, S.Kato, H.Uchiyama, T.Miyoshi-Akiyama, T.Papageorgiou, A.C.

(2007) J.Mol.Biol. 373: 1089

  • DOI: 10.1016/j.jmb.2007.08.024

  • PubMed Abstract: 
  • Bacterial superantigens are protein toxins with an ability to cause serious diseases in humans by activating a large number of T cells. Streptococcus dysgalactiae-derived mitogen (SDM) is a novel superantigen that is distinct from other known superan ...

    Bacterial superantigens are protein toxins with an ability to cause serious diseases in humans by activating a large number of T cells. Streptococcus dysgalactiae-derived mitogen (SDM) is a novel superantigen that is distinct from other known superantigens based on phylogenetic analysis. The X-ray structure of SDM has been determined at 1.95 A resolution. SDM shares the same characteristic fold with other superantigens, but it shows a major structural difference due to the lack of the alpha5 helix between the beta10 and beta11 strands. A bound zinc ion was identified in the structure at the C-terminal domain of the molecule. SDM appears to bind to the major histocompatibility complex class II beta-chain through the zinc-binding site, as described by mutagenesis data and structural comparisons. T-cell binding instead shows a significant difference compared to other superantigens. The mutation of Asn11 (a conserved residue that is known to be significant for T-cell-receptor binding in other superantigens) and Lys15 to Ala did not cause any decrease in the mitogenic activity of SDM. This observation and the lack of the alpha5 helix suggest alterations in T-cell-receptor binding.


    Organizational Affiliation

    Turku Center for Biotechnology, University of Turku and Abo Akademi University, PO Box 123, Tykistökatu 6, BioCity, Turku 20521, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITOGEN
A
213Streptococcus dysgalactiae subsp. dysgalactiaeMutation(s): 0 
Gene Names: sdm
Find proteins for Q8L3E1 (Streptococcus dysgalactiae subsp. dysgalactiae)
Go to UniProtKB:  Q8L3E1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.205 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 51.868α = 90.00
b = 51.868β = 90.00
c = 62.104γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance