2IAM

Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor

Deng, L.Langley, R.J.Brown, P.H.Xu, G.Teng, L.Wang, Q.Gonzales, M.I.Callender, G.G.Nishimura, M.I.Topalian, S.L.Mariuzza, R.A.

(2007) Nat Immunol 8: 398-408

  • DOI: https://doi.org/10.1038/ni1447
  • Primary Citation of Related Structures:  
    2IAL, 2IAM, 2IAN

  • PubMed Abstract: 

    Structural studies of complexes of T cell receptor (TCR) and peptide-major histocompatibility complex (MHC) have focused on TCRs specific for foreign antigens or native self. An unexplored category of TCRs includes those specific for self determinants bearing alterations resulting from disease, notably cancer. We determined here the structure of a human melanoma-specific TCR (E8) bound to the MHC molecule HLA-DR1 and an epitope from mutant triosephosphate isomerase. The structure had features intermediate between 'anti-foreign' and autoimmune TCR-peptide-MHC class II complexes that may reflect the hybrid nature of altered self. E8 manifested very low affinity for mutant triosephosphate isomerase-HLA-DR1 despite the highly tumor-reactive properties of E8 cells. A second TCR (G4) had even lower affinity but underwent peptide-specific formation of dimers, suggesting this as a mechanism for enhancing low-affinity TCR-peptide-MHC interactions for T cell activation.


  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain182Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA
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Find proteins for P01903 (Homo sapiens)
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Go to UniProtKB:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chain190Homo 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
15-mer peptide from Triosephosphate isomeraseC [auth P]15Homo sapiensMutation(s): 1 
Gene Names: TPI1TPI
EC: 5.3.1.1
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Find proteins for P60174 (Homo sapiens)
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GTEx:  ENSG00000111669 
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UniProt GroupP60174
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CD4+ T cell receptor E8 alpha chainD [auth C]202Homo sapiensMutation(s): 0 
UniProt
Find proteins for P01848 (Homo sapiens)
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UniProt GroupP01848
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CD4+ T cell receptor E8 beta chainE [auth D]240Homo sapiensMutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
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Go to UniProtKB:  P01850
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UniProt GroupP01850
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.391α = 90
b = 270.542β = 90
c = 97.396γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    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: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description