8VCY

Human TCR A2.13 in complex with DQ8-InsC8-15NPY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8.

Tran, M.T.Lim, J.J.Loh, T.J.Mannering, S.I.Rossjohn, J.Reid, H.H.

(2024) J Biol Chem 300: 107612-107612

  • DOI: https://doi.org/10.1016/j.jbc.2024.107612
  • Primary Citation of Related Structures:  
    8VCX, 8VCY, 8VD0, 8VD2, 8VDD, 8VDU

  • PubMed Abstract: 

    Type 1 diabetes (T1D) is a T cell-mediated autoimmune disease that has a strong HLA association, where a number of self-epitopes have been implicated in disease pathogenesis. Human pancreatic islet-infiltrating CD4 + T cell clones not only respond to proinsulin C-peptide (PI 40-54; GQVELGGGPGAGSLQ) but also cross-react with a hybrid insulin peptide (HIP; PI 40-47 -IAPP 74-80; GQVELGGG-NAVEVLK) presented by HLA-DQ8. How T cell receptors recognise self-peptide and cross-react to HIPs is unclear. We investigated the cross-reactivity of the CD4 + T cell clones reactive to native PI 40-54 epitope and multiple HIPs fused at the same N-terminus (PI 40-54 ) to the degradation products of two highly expressed pancreatic islet proteins, Neuropeptide Y (NPY 68-74 ) and amyloid polypeptide (IAPP 23-29 and IAPP 74-80 ). We observed that five out of the selected SKW3 T cell lines expressing TCRs isolated from CD4 + T cells of people with T1D responded to multiple HIPs. Despite shared TRAV26-1-TRBV5-1 gene usage in some T cells, these clones cross-reacted to varying degrees with the PI 40-54 and HIP epitopes. Crystal structures of two TRAV26-1 + -TRBV5-1 + T cell receptors (TCRs) in complex with PI 40-54 and HIPs bound to HLA-DQ8 revealed that the two TCRs had distinct mechanisms responsible for their differential recognition of the PI 40-54 and HIP epitopes. Alanine scanning mutagenesis of the PI 40-54 and HIPs determined that the P2, P7 and P8 residues in these epitopes were key determinants of TCR specificity. Accordingly, we provide a molecular basis for cross-reactivity towards native insulin and HIP epitopes presented by HLA-DQ8.


  • Organizational Affiliation

    Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia 3800.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-alpha chain185Homo sapiensMutation(s): 1 
Gene Names: HLA-DQA1
UniProt
Find proteins for Q30069 (Homo sapiens)
Explore Q30069 
Go to UniProtKB:  Q30069
Entity Groups  
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UniProt GroupQ30069
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-beta-1192Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1
UniProt
Find proteins for O19707 (Homo sapiens)
Explore O19707 
Go to UniProtKB:  O19707
Entity Groups  
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UniProt GroupO19707
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)15Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL-RECEPTOR, TCR A2.13 alpha203Homo sapiensMutation(s): 0 
Gene Names: TRAV26-1*01
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL-RECEPTOR, TCR A2.13 beta239Homo sapiensMutation(s): 0 
Gene Names: TRBV5-1*01
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth D],
L [auth D],
M [auth D],
P [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
J [auth D],
N [auth E],
O [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.803α = 90
b = 106.695β = 90
c = 132.962γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoXDSdata reduction
Cootmodel building
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia2008981
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1123586

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Database references
  • Version 1.2: 2024-09-04
    Changes: Database references