6TMO

Structure determination of an enhanced affinity TCR, a24b17, in complex with HLA-A*02:01 presenting a MART-1 peptide, EAAGIGILTV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy.

Crean, R.M.MacLachlan, B.J.Madura, F.Whalley, T.Rizkallah, P.J.Holland, C.J.McMurran, C.Harper, S.Godkin, A.Sewell, A.K.Pudney, C.R.van der Kamp, M.W.Cole, D.K.

(2020) Mol Ther Oncolytics 18: 443-456

  • DOI: 10.1016/j.omto.2020.07.008
  • Primary Citation of Related Structures:  
    6TMO

  • PubMed Abstract: 
  • Immuno-oncology approaches that utilize T cell receptors (TCRs) are becoming highly attractive because of their potential to target virtually all cellular proteins, including cancer-specific epitopes, via the recognition of peptide-human leukocyte an ...

    Immuno-oncology approaches that utilize T cell receptors (TCRs) are becoming highly attractive because of their potential to target virtually all cellular proteins, including cancer-specific epitopes, via the recognition of peptide-human leukocyte antigen (pHLA) complexes presented at the cell surface. However, because natural TCRs generally recognize cancer-derived pHLAs with very weak affinities, efforts have been made to enhance their binding strength, in some cases by several million-fold. In this study, we investigated the mechanisms underpinning human TCR affinity enhancement by comparing the crystal structures of engineered enhanced affinity TCRs with those of their wild-type progenitors. Additionally, we performed molecular dynamics simulations to better understand the energetic mechanisms driving the affinity enhancements. These data demonstrate that supra-physiological binding affinities can be achieved without altering native TCR-pHLA binding modes via relatively subtle modifications to the interface contacts, often driven through the addition of buried hydrophobic residues. Individual energetic components of the TCR-pHLA interaction governing affinity enhancements were distinct and highly variable for each TCR, often resulting from additive, or knock-on, effects beyond the mutated residues. This comprehensive analysis of affinity-enhanced TCRs has important implications for the future rational design of engineered TCRs as efficacious and safe drugs for cancer treatment.


    Organizational Affiliation

    Immunocore, Ltd., Abingdon, OX14 4RY, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class I antigenA276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
Find proteins for A0A5B8RNS7 (Homo sapiens)
Explore A0A5B8RNS7 
Go to UniProtKB:  A0A5B8RNS7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EAAGIGILTVC10Homo sapiensMutation(s): 0 
Gene Names: MLANAMART1
Find proteins for Q16655 (Homo sapiens)
Explore Q16655 
Go to UniProtKB:  Q16655
NIH Common Fund Data Resources
PHAROS  Q16655
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha chain of engineered high affinity T-cell receptorD197Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Beta chain of high affinity engineered T-cell receptorE244Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAM
Query on TAM

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A, E
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, D, E
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, D, E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.49α = 90
b = 121.49β = 90
c = 82.68γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references