8RYQ | pdb_00008ryq

Structure of S8-9F3 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.283 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Broadening alloselectivity of T cell receptors by structure guided engineering.

Karuppiah, V.Sangani, D.Whaley, L.Pengelly, R.Uluocak, P.Carreira, R.J.Hock, M.Cristina, P.D.Bartasun, P.Dobrinic, P.Smith, N.Barnbrook, K.Robinson, R.A.Harper, S.

(2024) Sci Rep 14: 26851-26851

  • DOI: https://doi.org/10.1038/s41598-024-75140-7
  • Primary Citation of Related Structures:  
    8RYM, 8RYN, 8RYO, 8RYP, 8RYQ

  • PubMed Abstract: 

    Specificity of a T cell receptor (TCR) is determined by the combination of its interactions to the peptide and human leukocyte antigen (HLA). TCR-based therapeutic molecules have to date targeted a single peptide in the context of a single HLA allele. Some peptides are presented on multiple HLA alleles, and by engineering TCRs for specific recognition of more than one allele, there is potential to expand the targetable patient population. Here, as a proof of concept, we studied two TCRs, S2 and S8, binding to the PRAME peptide antigen (ELFSYLIEK) presented by HLA alleles HLA-A*03:01 and HLA-A*11:01. By structure-guided affinity maturation targeting a specific residue on the HLA surface, we show that the affinity of the TCR can be modulated for different alleles. Using a combination of affinity maturation and functional T cell assay, we demonstrate that an engineered TCR can target the same peptide on two different HLA alleles with similar affinity and potency. This work highlights the importance of engineering alloselectivity for designing TCR based therapeutics suitable for differing global populations.


  • Organizational Affiliation
    • Immunocore Ltd, 92 Milton Park, Abingdon, Oxfordshire, OX14 4RY, UK. Vijaykumar.Karuppiah@immunocore.com.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen
A, F
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A583ZB34 (Homo sapiens)
Explore A0A583ZB34 
Go to UniProtKB:  A0A583ZB34
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UniProt GroupA0A583ZB34
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo 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 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ELFSYLIEK peptide
C, H
9Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alpha
D, I
200Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TCR beta
E, J
244Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.283 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.02α = 90.9
b = 88.89β = 98.54
c = 121.86γ = 97.72
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data 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: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-02-12
    Changes: Database references