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 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
T CELL RECEPTOR ALPHA CHAINA, G206Homo sapiensMutation(s): 0 
Gene Names: TRAC, TCRA
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T CELL RECEPTOR BETA CHAINB, H244Homo sapiensMutation(s): 0 
Gene Names: TRBC2, TCRBC2
Find proteins for A0A5B9 (Homo sapiens)
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PHAROS:  A0A5B9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ENTEROTOXIN BC, I238Staphylococcus aureusMutation(s): 0 
Gene Names: entB
Find proteins for P01552 (Staphylococcus aureus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIND, J182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
GTEx:  ENSG00000204287
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MHC CLASS II ANTIGENE, K190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P01911 (Homo sapiens)
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PHAROS:  P01911
GTEx:  ENSG00000196126
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
HEMAGGLUTININF, L13Influenza A virusMutation(s): 0 
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 M [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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