1AN8 | pdb_00001an8

CRYSTAL STRUCTURE OF THE STREPTOCOCCAL SUPERANTIGEN SPE-C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.210 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules.

Roussel, A.Anderson, B.F.Baker, H.M.Fraser, J.D.Baker, E.N.

(1997) Nat Struct Biol 4: 635-643

  • DOI: https://doi.org/10.1038/nsb0897-635
  • Primary Citation Related Structures: 
    1AN8

  • PubMed Abstract: 

    Bacterial superantigens are small proteins that have a very potent stimulatory effect on T lymphocytes through their ability to bind to both MHC class II molecules and T-cell receptors. We have determined the three-dimensional structure of a Streptococcal superantigen, SPE-C, at 2.4 A resolution. The structure shows that SPE-C has the usual superantigen fold, but that the surface that forms a generic, low-affinity MHC-binding site in other superantigens is here used to create a SPE-C dimer. Instead, MHC class II binding occurs through a zinc binding site that is analogous to a similar site in staphylococcal enterotoxin A. Consideration of the SPE-C dimer suggests a novel mechanism for promotion of MHC aggregation and T-cell activation.


  • Organizational Affiliation
    • Department of Biochemistry, Massey University, Palmerston North, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 24.38 kDa 
  • Atom Count: 1,842 
  • Modeled Residue Count: 206 
  • Deposited Residue Count: 208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
STREPTOCOCCAL PYROGENIC EXOTOXIN C208Streptococcus pyogenesMutation(s): 0 
UniProt
Find proteins for Q8NKX2 (Streptococcus pyogenes serotype M18 (strain MGAS8232))
Explore Q8NKX2 
Go to UniProtKB:  Q8NKX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NKX2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.210 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.41α = 90
b = 75.41β = 90
c = 168.87γ = 90
Software Package:
Software NamePurpose
CCP4model building
TNTrefinement
DENZOdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Other