6DFX

human diabetogenic TCR T1D3 in complex with DQ8-p8E9E peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 2.0 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: 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 ...

    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

    Structural Biology and Biochemistry program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II HLA-DQ-alpha chainA,
C [auth D]
188Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
UniProt
Find proteins for Q30069 (Homo sapiens)
Explore Q30069 
Go to UniProtKB:  Q30069
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UniProt GroupQ30069
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II antigenB,
D [auth E]
221Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt
Find proteins for U3PYM0 (Homo sapiens)
Explore U3PYM0 
Go to UniProtKB:  U3PYM0
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UniProt GroupU3PYM0
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T1D3 alpha chainE [auth G],
G [auth I]
207Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
T1D3 beta chainF [auth H],
H [auth J]
238Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.705α = 90
b = 88.896β = 104.26
c = 116.777γ = 90
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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary