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: 2.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.233 

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

  • 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 presen ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T CELL RECEPTOR ALPHA CHAIN
A, G
206Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T CELL RECEPTOR BETA CHAIN
B, H
244Homo sapiensMutation(s): 0 
Gene Names: TRBC2 (TCRBC2)
Find proteins for A0A5B9 (Homo sapiens)
Go to UniProtKB:  A0A5B9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ENTEROTOXIN B
C, I
238Staphylococcus aureusMutation(s): 0 
Gene Names: entB
Find proteins for P01552 (Staphylococcus aureus)
Go to UniProtKB:  P01552
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
D, J
182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MHC CLASS II ANTIGEN
E, K
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P04229 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P04229
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
HEMAGGLUTININ
F, L
13Influenza A virus (strain A/Aichi/2/1968 H3N2)Mutation(s): 0 
Gene Names: HA
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Go to UniProtKB:  P03437
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
E
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: 2.9 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.350α = 90.00
b = 217.650β = 99.82
c = 101.410γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references