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 the Department of Immunology, Kinki University School of Medicine, Osaka 589-8511, Japan, 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


View more in-depth experimental data

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