7NDT

UL40:01 TCR in complex with HLA-E with a non-natural amino acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition.

Barber, C.De Souza, V.A.Paterson, R.L.Martin-Urdiroz, M.Mulakkal, N.C.Srikannathasan, V.Connolly, M.Phillips, G.Foong-Leong, T.Pengelly, R.Karuppiah, V.Grant, T.Dembek, M.Verma, A.Gibbs-Howe, D.Blicher, T.H.Knox, A.Robinson, R.A.Cole, D.K.Leonard, S.

(2022) Eur J Immunol 52: 618-632

  • DOI: https://doi.org/10.1002/eji.202149745
  • Primary Citation of Related Structures:  
    6ZKW, 6ZKX, 6ZKY, 6ZKZ, 7NDQ, 7NDT, 7NDU

  • PubMed Abstract: 

    The nonpolymorphic class Ib molecule, HLA-E, primarily presents peptides from HLA class Ia leader peptides, providing an inhibitory signal to NK cells via CD94/NKG2 interactions. Although peptides of pathogenic origin can also be presented by HLA-E to T cells, the molecular basis underpinning their role in antigen surveillance is largely unknown. Here, we solved a co-complex crystal structure of a TCR with an HLA-E presented peptide (pHLA-E) from bacterial (Mycobacterium tuberculosis) origin, and the first TCR-pHLA-E complex with a noncanonically presented peptide from viral (HIV) origin. The structures provided a molecular foundation to develop a novel method to introduce cysteine traps using non-natural amino acid chemistry that stabilized pHLA-E complexes while maintaining native interface contacts between the TCRs and different pHLA-E complexes. These pHLA-E monomers could be used to isolate pHLA-E-specific T cells, with obvious utility for studying pHLA-E restricted T cells, and for the identification of putative therapeutic TCRs.


  • Organizational Affiliation

    Immunocore Ltd, Abingdon, Oxfordshire, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, alpha chain EA [auth AAA],
F [auth FFF]
277Homo sapiensMutation(s): 0 
Gene Names: HLA-EHLA-6.2HLAE
UniProt & NIH Common Fund Data Resources
Find proteins for P13747 (Homo sapiens)
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Go to UniProtKB:  P13747
PHAROS:  P13747
GTEx:  ENSG00000204592 
Entity Groups  
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UniProt GroupP13747
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinB [auth BBB],
G [auth GGG]
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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GTEx:  ENSG00000166710 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
UL40(15-23 H4C)C [auth CCC],
H [auth HHH]
9Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 26-1,T cell receptor alpha joining 37,T cell receptor alpha chain constantD [auth DDD],
I [auth III]
198Homo sapiensMutation(s): 3 
Gene Names: TRAV26-1TRAJ37TRACTCRA
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GTEx:  ENSG00000278661 
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PHAROS:  P01848
Find proteins for A0A087WT03 (Homo sapiens)
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GTEx:  ENSG00000211807 
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UniProt GroupsP01848A0A087X096A0A087WT03
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor beta variable 14,T cell receptor beta joining 2-3,T cell receptor beta constant 2E [auth EEE],
J [auth JJJ]
243Homo sapiensMutation(s): 3 
Gene Names: TRBV14TCRBV14S1TCRBV16S1A1N1TRBJ2-3hCG_2039521TRBC2TCRBC2
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Find proteins for A0A0B4J200 (Homo sapiens)
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GTEx:  ENSG00000211767 
Find proteins for A0A5B0 (Homo sapiens)
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PHAROS:  A0A5B0
GTEx:  ENSG00000275743 
Entity Groups  
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UniProt GroupsA0A5B0A0A5B9A0A0B4J200
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
QM8
Query on QM8
C [auth CCC],
H [auth HHH]
L-PEPTIDE LINKINGC6 H13 N O2 SALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.614α = 90
b = 76.577β = 107.639
c = 130.341γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 2.0: 2022-02-16
    Changes: Atomic model, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2022-04-20
    Changes: Database references
  • Version 2.2: 2022-07-27
    Changes: Derived calculations
  • Version 2.3: 2024-01-31
    Changes: Data collection, Refinement description