2ICW

Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC.

Wang, L.Zhao, Y.Li, Z.Guo, Y.Jones, L.L.Kranz, D.M.Mourad, W.Li, H.

(2007) Nat Struct Mol Biol 14: 169-171

  • DOI: https://doi.org/10.1038/nsmb1193
  • Primary Citation of Related Structures:  
    2ICW

  • PubMed Abstract: 

    'Superantigens' (SAgs) trigger the massive activation of T cells by simultaneous interactions with MHC and TCR receptors, leading to human diseases. Here we present the first crystal structure, at 2.5-A resolution, of a complete ternary complex between a SAg and its two receptors, HLA-DR1/HA and TCR. The most striking finding is that the SAg Mycoplasma arthritidis mitogen, unlike others, has direct contacts not only with TCR Vbeta but with TCR Valpha.


  • Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain
A, D
179Homo sapiensMutation(s): 3 
Gene Names: HLA-DRA
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chain
B, E
190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
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Go to UniProtKB:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
haemagglutinin peptide
C, F
13N/AMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mycoplasma arthritidis mitogen
G, H
213Metamycoplasma arthritidisMutation(s): 0 
UniProt
Find proteins for Q48898 (Metamycoplasma arthritidis)
Explore Q48898 
Go to UniProtKB:  Q48898
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UniProt GroupQ48898
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor alpha chain V
I, K
110Mus musculusMutation(s): 2 
UniProt
Find proteins for P01738 (Mus musculus)
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UniProt GroupP01738
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor beta chain V
J, L
113Mus musculusMutation(s): 3 
UniProt
Find proteins for A2NTY6 (Mus musculus)
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Go to UniProtKB:  A2NTY6
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UniProt GroupA2NTY6
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.516α = 110.27
b = 86.822β = 92.32
c = 116.981γ = 107.87
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection