4Z78

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.304 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide.

Motozono, C.Pearson, J.A.De Leenheer, E.Rizkallah, P.J.Beck, K.Trimby, A.Sewell, A.K.Wong, F.S.Cole, D.K.

(2015) J.Biol.Chem. 290: 18924-18933

  • DOI: 10.1074/jbc.M114.622522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The non-obese diabetic mouse model of type 1 diabetes continues to be an important tool for delineating the role of T-cell-mediated destruction of pancreatic β-cells. However, little is known about the molecular mechanisms that enable this disease pa ...

    The non-obese diabetic mouse model of type 1 diabetes continues to be an important tool for delineating the role of T-cell-mediated destruction of pancreatic β-cells. However, little is known about the molecular mechanisms that enable this disease pathway. We show that insulin reactivity by a CD8(+) T-cell clone, known to induce type 1 diabetes, is characterized by weak T-cell antigen receptor binding to a relatively unstable peptide-MHC. The structure of the native 9- and 10-mer insulin epitopes demonstrated that peptide residues 7 and 8 form a prominent solvent-exposed bulge that could potentially be the main focus of T-cell receptor binding. The C terminus of the peptide governed peptide-MHC stability. Unexpectedly, we further demonstrate a novel mode of flexible peptide presentation in which the MHC peptide-binding groove is able to "open the back door" to accommodate extra C-terminal peptide residues.


    Organizational Affiliation

    From the Division of Infection and Immunity and coledk@cf.ac.uk.,the Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, United Kingdom.,the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.,From the Division of Infection and Immunity and the Department of Immunology, Kinki University School of Medicine, Osaka 589-8511, Japan, and.,the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom, wongfs@cf.ac.uk.,From the Division of Infection and Immunity and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, K-D alpha chain
A, D, G
277Mus musculusMutation(s): 0 
Gene Names: H2-K1 (H2-K)
Find proteins for P01902 (Mus musculus)
Go to UniProtKB:  P01902
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E, H
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Insulin
C, F, I
10Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D, E, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, D, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.304 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.170α = 90.00
b = 151.570β = 90.00
c = 182.230γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references
  • Version 1.2: 2015-08-12
    Type: Database references