6DFS

mouse TCR I.29 in complex with IAg7-p8E9E6ss


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes.

Wang, Y.Sosinowski, T.Novikov, A.Crawford, F.White, J.Jin, N.Liu, Z.Zou, J.Neau, D.Davidson, H.W.Nakayama, M.Kwok, W.W.Gapin, L.Marrack, P.Kappler, J.W.Dai, S.

(2019) Sci Immunol 4

  • DOI: https://doi.org/10.1126/sciimmunol.aav7517
  • Primary Citation of Related Structures:  
    6DFQ, 6DFS, 6DFV, 6DFW, 6DFX

  • PubMed Abstract: 

    In type 1 diabetes (T1D), proinsulin is a major autoantigen and the insulin B:9-23 peptide contains epitopes for CD4 + T cells in both mice and humans. This peptide requires carboxyl-terminal mutations for uniform binding in the proper position within the mouse IA g7 or human DQ8 major histocompatibility complex (MHC) class II (MHCII) peptide grooves and for strong CD4 + T cell stimulation. Here, we present crystal structures showing how these mutations control CD4 + T cell receptor (TCR) binding to these MHCII-peptide complexes. Our data reveal stricking similarities between mouse and human CD4 + TCRs in their interactions with these ligands. We also show how fusions between fragments of B:9-23 and of proinsulin C-peptide create chimeric peptides with activities as strong or stronger than the mutated insulin peptides. We propose transpeptidation in the lysosome as a mechanism that could accomplish these fusions in vivo, similar to the creation of fused peptide epitopes for MHCI presentation shown to occur by transpeptidation in the proteasome. Were this mechanism limited to the pancreas and absent in the thymus, it could provide an explanation for how diabetogenic T cells escape negative selection during development but find their modified target antigens in the pancreas to cause T1D.


  • Organizational Affiliation

    Department of Biomedical Research, National Jewish Health, Denver, CO 80206, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mouse TCR alpha chain210Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mouse TCR beta chain242Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class II histocompatibility antigen, A-D alpha chain183Mus musculusMutation(s): 0 
Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus)
Explore P04228 
Go to UniProtKB:  P04228
Entity Groups  
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UniProt GroupP04228
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H2-Ab1 protein215Mus musculusMutation(s): 0 
Gene Names: H2-Ab1
UniProt
Find proteins for Q31135 (Mus musculus)
Explore Q31135 
Go to UniProtKB:  Q31135
Entity Groups  
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UniProt GroupQ31135
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.518α = 90
b = 269.518β = 90
c = 45.639γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary