9HI7 | pdb_00009hi7

Structure of MC.7.G5 T cell receptor in complex with MR1 R9H

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 
    0.296 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Molecular basis underpinning MR1 allomorph recognition by an MR1-restricted T cell receptor.

Suckling, R.J., Pamukcu, C., Simmons, R.A., Fonseca, D., Grant, E., Harrison, R., Shaikh, S.A., Khanolkar, R.C., Ghadbane, H., Creese, A., Hock, M., Gligoris, T.G., Lepore, M., Karuppiah, V., Salio, M.

(2025) Front Immunol 16: 1547664-1547664

  • DOI: https://doi.org/10.3389/fimmu.2025.1547664
  • Primary Citation Related Structures: 
    9HI7

  • PubMed Abstract: 

    The MHC-class-I-related molecule MR1 presents small metabolites of microbial and self-origin to T cells bearing semi-invariant or variant T cell receptors. One such T cell receptor, MC.7.G5, was previously shown to confer broad MR1-restricted reactivity to tumor cells but not normal cells, sparking interest in the development of non-MHC-restricted immunotherapy approaches. Here we provide cellular, biophysical, and crystallographic evidence that the MC.7.G5 TCR does not have pan-cancer specificity but is restricted to a rare allomorph of MR1, bearing the R9H mutation. Our results underscore the importance of in-depth characterization of MR1-reactive TCRs against targets expressing the full repertoire of MR1 allomorphs.

    • Organizational Affiliation: 
    • Immunocore Ltd., Abingdon, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 193.02 kDa 
  • Atom Count: 13,002 
  • Modeled Residue Count: 1,603 
  • Deposited Residue Count: 1,678 
  • Unique protein chains: 4

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major histocompatibility complex class I-related gene proteinA,
E [auth F]		290Homo sapiensMutation(s): 1 
Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens)
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Go to UniProtKB:  Q95460
PHAROS:  Q95460
GTEx:  ENSG00000153029 
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UniProt GroupQ95460
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB,
F [auth G]		100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor alpha chain MC.7.G5C [auth D],
G [auth H]		201Homo sapiensMutation(s): 0 
Gene Names: TRA
UniProt
Find proteins for P0DTU3 (Homo sapiens)
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UniProt GroupP0DTU3
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
T cell receptor beta chain MC.7.G5D [auth E],
H [auth I]		248Homo sapiensMutation(s): 0 
Gene Names: TRB
UniProt
Find proteins for P0DTU4 (Homo sapiens)
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UniProt GroupP0DTU4
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.296 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.03α = 90
b = 113.202β = 90.73
c = 130.363γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release