4Z78

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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:  
    4WDI, 4Z76, 4Z78

  • 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 pathway ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-D alpha chainA, D, G277Mus musculusMutation(s): 0 
Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01902 (Mus musculus)
Explore P01902 
Go to UniProtKB:  P01902
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB, E, H100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
InsulinC, F, I10Homo sapiensMutation(s): 0 
Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
PHAROS:  P01308
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
O [auth A] , P [auth A] , Q [auth A] , R [auth A] , U [auth D] , V [auth D] , W [auth D] , X [auth D] , 
O [auth A], P [auth A], Q [auth A], R [auth A], U [auth D], V [auth D], W [auth D], X [auth D], Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
BA [auth H], CA [auth H], M [auth A], N [auth A], T [auth D], Y [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth H], J [auth A], K [auth A], L [auth A], S [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.17α = 90
b = 151.57β = 90
c = 182.23γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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