3UTS | pdb_00003uts

1E6-A*0201-ALWGPDPAAA Complex, Monoclinic


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.71 Å
  • R-Value Free:&nbsp
    0.269 (Depositor), 0.263 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.201 (Depositor), 0.201 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.205&nbsp(Depositor)&nbsp

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.2 of the entry. See complete&nbsphistory.&nbsp


Literature

Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.

Bulek, A.M.,&nbspCole, D.K.,&nbspSkowera, A.,&nbspDolton, G.,&nbspGras, S.,&nbspMadura, F.,&nbspFuller, A.,&nbspMiles, J.J.,&nbspGostick, E.,&nbspPrice, D.A.,&nbspDrijfhout, J.W.,&nbspKnight, R.R.,&nbspHuang, G.C.,&nbspLissin, N.,&nbspMolloy, P.E.,&nbspWooldridge, L.,&nbspJakobsen, B.K.,&nbspRossjohn, J.,&nbspPeakman, M.,&nbspRizkallah, P.J.,&nbspSewell, A.K.

(2012) Nat Immunol&nbsp13: 283-289

  • DOI:&nbsphttps://doi.org/10.1038/ni.2206
  • Primary Citation of Related Structures: &nbsp
    3UTP, 3UTQ, 3UTS, 3UTT

  • PubMed Abstract:&nbsp

    The structural characteristics of the engagement of major histocompatibility complex (MHC) class II-restricted self antigens by autoreactive T cell antigen receptors (TCRs) is established, but how autoimmune TCRs interact with complexes of self peptide and MHC class I has been unclear. Here we examined how CD8(+) T cells kill human islet beta cells in type 1 diabetes via recognition of a human leukocyte antigen HLA-A*0201-restricted glucose-sensitive preproinsulin peptide by the autoreactive TCR 1E6. Rigid 'lock-and-key' binding underpinned the 1E6-HLA-A*0201-peptide interaction, whereby 1E6 docked similarly to most MHC class I-restricted TCRs. However, this interaction was extraordinarily weak because of limited contacts with MHC class I. TCR binding was highly peptide centric, dominated by two residues of the complementarity-determining region 3 (CDR3) loops that acted as an 'aromatic-cap' over the complex of peptide and MHC class I (pMHCI). Thus, highly focused peptide-centric interactions associated with suboptimal TCR-pMHCI binding affinities might lead to thymic escape and potential CD8(+) T cell-mediated autoreactivity.


  • Organizational Affiliation:&nbsp

    Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.


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
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin
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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
1E6 TCR Alpha Chain
D, I
201Homo sapiensMutation(s): 0&nbsp
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
1E6 TCR Beta Chain
E, J
246Homo sapiensMutation(s): 0&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.71 Å
  • R-Value Free:&nbsp 0.269 (Depositor), 0.263 (DCC)&nbsp
  • R-Value Work:&nbsp 0.201 (Depositor), 0.201 (DCC)&nbsp
  • R-Value Observed:&nbsp0.205&nbsp(Depositor)&nbsp
Space Group:&nbspP 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.68α = 90
b = 84.59β = 90.03
c = 126.28γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection
xia2data reduction
PHASERphasing

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-03-07
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary