7N5Q

Peptide-MHC complex of mouse H2-Db presenting PA224 with E4C mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
Molecule Chains  Sequence Length Organism Details Image
H-2 class I histocompatibility antigen, D-B alpha chain A,
D [auth F]
281 Mus musculus Mutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Entity Groups  
Sequence Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group P01899
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
Molecule Chains  Sequence Length Organism Details Image
Beta-2-microglobulin B,
E [auth G]
100 Homo sapiens Mutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
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UniProt Group P61769
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  • Reference Sequence

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Entity ID: 3
Molecule Chains  Sequence Length Organism Details Image
peptide from Polymerase acidic protein C,
F [auth H]
10 Influenza A virus Mutation(s): 1 
UniProt
Find proteins for O89752 (Influenza A virus (strain A/Hong Kong/156/1997 H5N1 genotype Gs/Gd))
Explore O89752 
Go to UniProtKB:  O89752
Entity Groups  
Sequence Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group O89752
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
ID Chains  Name / Formula / InChI Key 2D Diagram 3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
R [auth G]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth F],
S [auth G],
T [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å ) Angle ( ˚ )
a = 46.41 α = 111.33
b = 61.77 β = 91.19
c = 71.68 γ = 91.77
Software Package:
Software Name Purpose
BUSTER refinement
PDB_EXTRACT data extraction
XDS data reduction
Aimless data scaling
PHASER phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding Organization Location Grant Number
National Health and Medical Research Council (NHMRC, Australia) Australia 1159272

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