6XCO

Immune receptor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

T cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8.

Tran, M.T.Faridi, P.Lim, J.J.Ting, Y.T.Onwukwe, G.Bhattacharjee, P.Jones, C.M.Tresoldi, E.Cameron, F.J.La Gruta, N.L.Purcell, A.W.Mannering, S.I.Rossjohn, J.Reid, H.H.

(2021) Nat Commun 12: 5110-5110

  • DOI: https://doi.org/10.1038/s41467-021-25404-x
  • Primary Citation of Related Structures:  
    6XC9, 6XCO, 6XCP

  • PubMed Abstract: 

    HLA-DQ8, a genetic risk factor in type I diabetes (T1D), presents hybrid insulin peptides (HIPs) to autoreactive CD4+ T cells. The abundance of spliced peptides binding to HLA-DQ8 and how they are subsequently recognised by the autoreactive T cell repertoire is unknown. Here we report, the HIP (GQVELGGGNAVEVLK), derived from splicing of insulin and islet amyloid polypeptides, generates a preferred peptide-binding motif for HLA-DQ8. HLA-DQ8-HIP tetramer + T cells from the peripheral blood of a T1D patient are characterised by repeated TRBV5 usage, which matches the TCR bias of CD4+ T cells reactive to the HIP peptide isolated from the pancreatic islets of a patient with T1D. The crystal structure of three TRBV5+ TCR-HLA-DQ8-HIP complexes shows that the TRBV5-encoded TCR β-chain forms a common landing pad on the HLA-DQ8 molecule. The N- and C-termini of the HIP is recognised predominantly by the TCR α-chain and TCR β-chain, respectively, in all three TCR ternary complexes. Accordingly, TRBV5 + TCR recognition of HIP peptides might occur via a 'polarised' mechanism, whereby each chain within the αβTCR heterodimer recognises distinct origins of the spliced peptide presented by HLA-DQ8.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class II HLA-DQ-alpha chain193Homo 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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hybrid Insulin Peptide, MHC class II HLA-DQ-beta-1 fusion230Homo sapiensMutation(s): 0 
UniProt
Find proteins for O19707 (Homo sapiens)
Explore O19707 
Go to UniProtKB:  O19707
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UniProt GroupO19707
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL-RECEPTOR, A1.9-alpha chainC [auth D]205Homo sapiensMutation(s): 0 
Gene Names: TRAV20*02
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL-RECEPTOR, A1.9-beta chainD [auth E]240Homo 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 
E [auth A],
F [auth A],
I [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CAC
Query on CAC

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H [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL
Query on GOL

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G [auth A]
J [auth B]
K [auth D]
L [auth D]
M [auth E]
G [auth A],
J [auth B],
K [auth D],
L [auth D],
M [auth E],
N [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.288α = 90
b = 104.31β = 114.914
c = 69.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata 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)AustraliaAPP1123586

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2022-01-26
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description