1B1Z | pdb_00001b1z

STREPTOCOCCAL PYROGENIC EXOTOXIN A1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.274 (Depositor) 
  • R-Value Work: 
    0.194 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

Structural basis for the recognition of superantigen streptococcal pyrogenic exotoxin A (SpeA1) by MHC class II molecules and T-cell receptors.

Papageorgiou, A.C.Collins, C.M.Gutman, D.M.Kline, J.B.O'Brien, S.M.Tranter, H.S.Acharya, K.R.

(1999) EMBO J 18: 9-21

  • DOI: https://doi.org/10.1093/emboj/18.1.9
  • Primary Citation Related Structures: 
    1B1Z

  • PubMed Abstract: 

    Streptococcal pyrogenic exotoxin A (SpeA) is a superantigen produced by Streptococcus pyogenes and is associated with severe infections characterized by rash, hypotension, multiorgan failure and a high mortality rate. In this study, an allelic form of this toxin, SpeA1, was crystallized with four molecules in the crystallographic asymmetric unit and its crystal structure was determined at 2.6 A resolution. The crystallographic R-factor was 19.4% (33 497 reflections) for 7031 protein atoms and 88 water molecules. The overall structure of SpeA1 is considerably similar to that of other prototype microbial superantigens, either of staphylococcal or streptococcal origin, but has greatest similarity to staphylococcal enterotoxin C (SEC). Based on structural and mutagenesis data, we have mapped several important residues on the toxin molecule, which are involved in the recognition of major histocompatibility complex (MHC) class II molecules and T-cell receptors. Also, the toxin appears to possess a potential zinc-binding site which may have implications in binding to particular MHC class II molecules. Finally, we propose models for SpeA1-MHC class II and SpeA1-T-cell receptor association and the relevance of this phenomenon to the superantigenic action of this toxin is considered.


  • Organizational Affiliation
    • Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.

Macromolecule Content 

  • Total Structure Weight: 102.25 kDa 
  • Atom Count: 7,114 
  • Modeled Residue Count: 872 
  • Deposited Residue Count: 876 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (TOXIN)
A, B, C, D
219Streptococcus pyogenesMutation(s): 0 
UniProt
Find proteins for P0DJY7 (Streptococcus pyogenes)
Explore P0DJY7 
Go to UniProtKB:  P0DJY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DJY7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.274 (Depositor) 
  • R-Value Work:  0.194 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.4α = 90
b = 101β = 90
c = 81.8γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-24
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary