5HYJ | pdb_00005hyj

1E6 TCR in Complex with HLA-A02 carrying AQWGPDPAAA


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.06 Å
  • R-Value Free:&nbsp
    0.293 (Depositor), 0.290 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.212 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.216&nbsp(Depositor)&nbsp

Starting Models: experimental
View more details

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.4 of the entry. See complete&nbsphistory.&nbsp


Literature

A "hotspot" for autoimmune T cells in type 1 diabetes.

Stadinski, B.D.,&nbspObst, R.,&nbspHuseby, E.S.

(2016) J Clin Invest&nbsp126: 2040-2042

  • DOI:&nbsphttps://doi.org/10.1172/JCI88165
  • Primary Citation of Related Structures: &nbsp
    5HYJ

  • PubMed Abstract:&nbsp

    The ability of a single T cell antigen receptor (TCR) to cross-react with multiple antigens allows the finite number of T cells within an organism to respond to the compendium of pathogen challenges faced during a lifetime. Effective immune surveillance, however, comes at a price. TCR cross-reactivity can allow molecular mimics to spuriously activate autoimmune T cells; it also underlies T cell rejection of organ transplants and drives graft-versus-host disease. In this issue of the JCI, Cole and colleagues provide insight into how an insulin-reactive T cell cross-reacts with pathogen-derived antigens by focusing on a limited portion of the peptides to provide a hotspot for binding. These findings dovetail with recent studies of alloreactive and autoimmune TCRs and suggest that the biochemical principles that govern conventional protein-protein interactions may allow the specificity and cross-reactivity profiles of T cells to be predicted.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain
A, F
276Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspHLA-A,&nbspHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP04439&nbsp(Homo sapiens)
Explore&nbspP04439&nbsp
Go to UniProtKB: &nbspP04439
PHAROS: &nbspP04439
GTEx: &nbspENSG00000206503&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspB2M,&nbspCDABP0092,&nbspHDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP61769&nbsp(Homo sapiens)
Explore&nbspP61769&nbsp
Go to UniProtKB: &nbspP61769
PHAROS: &nbspP61769
GTEx: &nbspENSG00000166710&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-GLN-TRP-GLY-PRO-ASP-PRO-ALA-ALA-ALA
C, H
10Homo sapiensMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01308&nbsp(Homo sapiens)
Explore&nbspP01308&nbsp
Go to UniProtKB: &nbspP01308
PHAROS: &nbspP01308
GTEx: &nbspENSG00000254647&nbsp
Entity Groups &nbsp
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UniProt GroupP01308
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Human T-cell Receptor, Class I, Light alpha Chain
D, I
193Homo sapiensMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspA0A0B4J271&nbsp(Homo sapiens)
Explore&nbspA0A0B4J271&nbsp
Go to UniProtKB: &nbspA0A0B4J271
PHAROS: &nbspA0A0B4J271
GTEx: &nbspENSG00000211794&nbsp
Find proteins for&nbspP01848&nbsp(Homo sapiens)
Explore&nbspP01848&nbsp
Go to UniProtKB: &nbspP01848
PHAROS: &nbspP01848
Entity Groups &nbsp
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UniProt GroupsA0A0B4J271P01848
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Human T-cell Receptor, Class I, Heavy beta Chain
E, J
246Homo sapiensMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspA0A0B4J2E0&nbsp(Homo sapiens)
Explore&nbspA0A0B4J2E0&nbsp
Go to UniProtKB: &nbspA0A0B4J2E0
GTEx: &nbspENSG00000276953&nbsp
Find proteins for&nbspA0A5B9&nbsp(Homo sapiens)
Explore&nbspA0A5B9&nbsp
Go to UniProtKB: &nbspA0A5B9
PHAROS: &nbspA0A5B9
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0B4J2E0A0A5B9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.06 Å
  • R-Value Free:&nbsp 0.293 (Depositor), 0.290 (DCC)&nbsp
  • R-Value Work:&nbsp 0.212 (Depositor), 0.210 (DCC)&nbsp
  • R-Value Observed:&nbsp0.216&nbsp(Depositor)&nbsp
Space Group:&nbspP 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.44α = 97.29
b = 97.31β = 97.66
c = 121.37γ = 92.73
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-08
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary