7N5C

6218 TCR in complex with H2Db PA with an engineered TCR-pMHC disulfide bond


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus.

Szeto, C.Zareie, P.Wirasinha, R.C.Zhang, J.B.Nguyen, A.T.Riboldi-Tunnicliffe, A.La Gruta, N.L.Gras, S.Daley, S.R.

(2022) Nat Commun 13: 4951-4951

  • DOI: https://doi.org/10.1038/s41467-022-32692-4
  • Primary Citation of Related Structures:  
    7N4K, 7N5C, 7N5P, 7N5Q

  • PubMed Abstract: 

    Interactions between a T cell receptor (TCR) and a peptide-major histocompatibility complex (pMHC) ligand are typically mediated by noncovalent bonds. By studying T cells expressing natural or engineered TCRs, here we describe covalent TCR-pMHC interactions that involve a cysteine-cysteine disulfide bond between the TCR and the peptide. By introducing cysteines into a known TCR-pMHC combination, we demonstrate that disulfide bond formation does not require structural rearrangement of the TCR or the peptide. We further show these disulfide bonds still form even when the initial affinity of the TCR-pMHC interaction is low. Accordingly, TCR-peptide disulfide bonds facilitate T cell activation by pMHC ligands with a wide spectrum of affinities for the TCR. Physiologically, this mechanism induces strong Zap70-dependent TCR signaling, which triggers T cell deletion or agonist selection in the thymus cortex. Covalent TCR-pMHC interactions may thus underlie a physiological T cell activation mechanism that has applications in basic immunology and potentially in immunotherapy.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain277Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
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UniProt GroupP01899
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
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Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
peptide from Polymerase acidic protein10Influenza A virusMutation(s): 1 
UniProt
Find proteins for O89752 (Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd))
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UniProt GroupO89752
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of T cell receptor alpha variable 21-DV12 with T-cell receptor, sp3.4 alpha chain204Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav21-dv12
UniProt
Find proteins for K7N5N2 (Homo sapiens)
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Find proteins for A0A075B6C4 (Mus musculus)
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UniProt GroupsK7N5N2A0A075B6C4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein of T cell receptor beta, variable 29 and Human nkt tcr beta chain240Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trbv29B2MHDCMA22P
UniProt
Find proteins for A0A0G2LB96 (Mus musculus)
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Find proteins for K7N5M4 (Homo sapiens)
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Go to UniProtKB:  K7N5M4
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UniProt GroupsK7N5M4A0A0G2LB96
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth E]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.086α = 90
b = 74.113β = 99.34
c = 114.295γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1159272

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description