4C56

X-ray structure of the complex between staphylococcal enterotoxin B, T cell receptor and major histocompatibility complex class II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Superantigen Staphylococcal Enterotoxin B in Complex with Tcr and Peptide-Mhc Demonstrates Absence of Tcr-Peptide Contacts.

Rodstrom, K.E.J.Elbing, K.Lindkvist-Petersson, K.

(2014) J Immunol 193: 1998

  • DOI: https://doi.org/10.4049/jimmunol.1401268
  • Primary Citation of Related Structures:  
    4C56

  • PubMed Abstract: 

    Superantigens are immune-stimulatory toxins produced by Staphylococcus aureus, which are able to interact with host immune receptors to induce a massive release of cytokines, causing toxic shock syndrome and possibly death. In this article, we present the x-ray structure of staphylococcal enterotoxin B (SEB) in complex with its receptors, the TCR and MHC class II, forming a ternary complex. The structure, in combination with functional analyses, clearly shows how SEB adopts a wedge-like position when binding to the β-chain of TCR, allowing for an interaction between the α-chain of TCR and MHC. Furthermore, the binding mode also circumvents contact between TCR and the peptide presented by MHC, which enables SEB to initiate a peptide-independent activation of T cells.


  • Organizational Affiliation

    Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T CELL RECEPTOR ALPHA CHAIN
A, G
206Homo sapiensMutation(s): 0 
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PHAROS:  P01848
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UniProt GroupP01848
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T CELL RECEPTOR BETA CHAIN
B, H
244Homo sapiensMutation(s): 0 
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PHAROS:  A0A5B9
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UniProt GroupA0A5B9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ENTEROTOXIN B
C, I
238Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for P01552 (Staphylococcus aureus)
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UniProt GroupP01552
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
D, J
182Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204287 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MHC CLASS II ANTIGEN
E, K
190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000196126 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ
F, L
13Influenza A virusMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.35α = 90
b = 217.65β = 99.82
c = 101.41γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description