7RK7 | pdb_00007rk7

The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 
    0.255 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7RK7

This is version 1.3 of the entry. See complete history

Literature

A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry.

Singh, N.K.Alonso, J.A.Devlin, J.R.Keller, G.L.J.Gray, G.I.Chiranjivi, A.K.Foote, S.G.Landau, L.M.Arbuiso, A.G.Weiss, L.I.Rosenberg, A.M.Hellman, L.M.Nishimura, M.I.Baker, B.M.

(2022) Nat Commun 13: 7189-7189

  • DOI: https://doi.org/10.1038/s41467-022-34896-0
  • Primary Citation Related Structures: 
    7RK7

  • PubMed Abstract: 

    MHC restriction, which describes the binding of TCRs from CD4 + T cells to class II MHC proteins and TCRs from CD8 + T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4 + T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.


  • Organizational Affiliation
    • Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.

Macromolecule Content 

  • Total Structure Weight: 97.04 kDa 
  • Atom Count: 6,295 
  • Modeled Residue Count: 773 
  • Deposited Residue Count: 851 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A alpha chain275Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosinase peptide9Homo sapiensMutation(s): 1 
EC: 1.14.18.1
UniProt & NIH Common Fund Data Resources
Find proteins for P14679 (Homo sapiens)
Explore P14679 
Go to UniProtKB:  P14679
PHAROS:  P14679
GTEx:  ENSG00000077498 
Entity Groups
UniProt GroupP14679
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
TIL1383i (h3T) T cell receptor alpha chain214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
TIL1383i (h3T) T cell receptor beta chain253Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free:  0.255 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.738α = 90
b = 74.428β = 93.487
c = 131.058γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118166

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary
  • Version 1.3: 2025-10-08
    Changes: Database references