5C0D | pdb_00005c0d

HLA-A02 carrying AQWGPDPAAA


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.68 Å
  • R-Value Free:&nbsp
    0.214 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.172 (Depositor), 0.180 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.174&nbsp(Depositor)&nbsp

Starting Model: experimental
View more details

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


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


Literature

Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.

Cole, D.K.,&nbspBulek, A.M.,&nbspDolton, G.,&nbspSchauenberg, A.J.,&nbspSzomolay, B.,&nbspRittase, W.,&nbspTrimby, A.,&nbspJothikumar, P.,&nbspFuller, A.,&nbspSkowera, A.,&nbspRossjohn, J.,&nbspZhu, C.,&nbspMiles, J.J.,&nbspPeakman, M.,&nbspWooldridge, L.,&nbspRizkallah, P.J.,&nbspSewell, A.K.

(2016) J Clin Invest&nbsp126: 2191-2204

  • DOI:&nbsphttps://doi.org/10.1172/JCI85679
  • Primary Citation of Related Structures: &nbsp
    5C07, 5C08, 5C09, 5C0A, 5C0B, 5C0C, 5C0D, 5C0E, 5C0F, 5C0G, 5C0I, 5C0J, 5N1Y

  • PubMed Abstract:&nbsp

    The cross-reactivity of T cells with pathogen- and self-derived peptides has been implicated as a pathway involved in the development of autoimmunity. However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide-major histocompatibility complexes (pMHC) are unclear. Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I-restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key-like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity; this engagement was governed though an energetic switch from an enthalpically to entropically driven interaction compared with the natural autoimmune ligand. Together, these data highlight how T cell cross-reactivity with pathogen-derived antigens might break self-tolerance to induce autoimmune disease.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain276Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo 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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Marker peptide10Homo 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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.68 Å
  • R-Value Free:&nbsp 0.214 (Depositor), 0.220 (DCC)&nbsp
  • R-Value Work:&nbsp 0.172 (Depositor), 0.180 (DCC)&nbsp
  • R-Value Observed:&nbsp0.174&nbsp(Depositor)&nbsp
Space Group:&nbspP 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.84α = 90
b = 81.15β = 112.32
c = 56.19γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

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: 2024-10-16
    Changes: Structure summary