4C56 | pdb_00004c56

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 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 247.31 kDa 
  • Atom Count: 16,311 
  • Modeled Residue Count: 2,078 
  • Deposited Residue Count: 2,146 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T CELL RECEPTOR ALPHA CHAIN
A, G
206Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
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PHAROS:  P01848
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UniProt GroupP01848
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
T CELL RECEPTOR BETA CHAIN
B, H
244Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens)
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PHAROS:  A0A5B9
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UniProt GroupA0A5B9
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Reference Sequence
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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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Reference Sequence
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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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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC CLASS II ANTIGEN
E, K
190Homo sapiensMutation(s): 0 
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PHAROS:  P01911
GTEx:  ENSG00000196126 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
HEMAGGLUTININ
F, L
13Influenza A virusMutation(s): 0 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
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Reference Sequence

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 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
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
  • Version 1.3: 2024-11-06
    Changes: Structure summary