3UTP | pdb_00003utp

1E6 TCR specific for HLA-A*0201-ALWGPDPAAA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.291 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3UTP

This is version 1.2 of the entry. See complete history

Literature

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

Bulek, A.M.Cole, D.K.Skowera, A.Dolton, G.Gras, S.Madura, F.Fuller, A.Miles, J.J.Gostick, E.Price, D.A.Drijfhout, J.W.Knight, R.R.Huang, G.C.Lissin, N.Molloy, P.E.Wooldridge, L.Jakobsen, B.K.Rossjohn, J.Peakman, M.Rizkallah, P.J.Sewell, A.K.

(2012) Nat Immunol 13: 283-289

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

  • PubMed Abstract: 

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

Macromolecule Content 

  • Total Structure Weight: 102.54 kDa 
  • Atom Count: 7,261 
  • Modeled Residue Count: 892 
  • Deposited Residue Count: 894 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1E6 TCR alpha chainA [auth D],
C [auth K]
201Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
1E6 TCR beta chainB [auth E],
D [auth L]
246Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTB

Query on BTB



Download:Ideal Coordinates CCD File
H [auth E]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth D]
G [auth D]
I [auth E]
J [auth E]
K [auth E]
F [auth D],
G [auth D],
I [auth E],
J [auth E],
K [auth E],
M [auth K],
N [auth K],
O [auth L],
P [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth D],
L [auth K]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.291 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.03α = 90
b = 43.26β = 101.25
c = 124.71γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

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: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary