6DKP

The complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, human Class I MHC HLA-A2 and MART-1(26-35)(A27L) peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.

Hellman, L.M.Foley, K.C.Singh, N.K.Alonso, J.A.Riley, T.P.Devlin, J.R.Ayres, C.M.Keller, G.L.J.Zhang, Y.Vander Kooi, C.W.Nishimura, M.I.Baker, B.M.

(2019) Mol Ther 27: 300-313

  • DOI: 10.1016/j.ymthe.2018.12.010
  • Primary Citation of Related Structures:  
    6DKP, 6D78

  • PubMed Abstract: 
  • T cell receptors (TCRs) have emerged as a new class of immunological therapeutics. However, though antigen specificity is a hallmark of adaptive immunity, TCRs themselves do not possess the high specificity of monoclonal antibodies. Although a necess ...

    T cell receptors (TCRs) have emerged as a new class of immunological therapeutics. However, though antigen specificity is a hallmark of adaptive immunity, TCRs themselves do not possess the high specificity of monoclonal antibodies. Although a necessary function of T cell biology, the resulting cross-reactivity presents a significant challenge for TCR-based therapeutic development, as it creates the potential for off-target recognition and immune toxicity. Efforts to enhance TCR specificity by mimicking the antibody maturation process and enhancing affinity can inadvertently exacerbate TCR cross-reactivity. Here we demonstrate this concern by showing that even peptide-targeted mutations in the TCR can introduce new reactivities against peptides that bear similarity to the original target. To counteract this, we explored a novel structure-guided approach for enhancing TCR specificity independent of affinity. Tested with the MART-1-specific TCR DMF5, our approach had a small but discernible impact on cross-reactivity toward MART-1 homologs yet was able to eliminate DMF5 cross-recognition of more divergent, unrelated epitopes. Our study provides a proof of principle for the use of advanced structure-guided design techniques for improving TCR specificity, and it suggests new ways forward for enhancing TCRs for therapeutic use.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA. Electronic address: brian-baker@nd.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
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PHAROS  P04439
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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)
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PHAROS  P61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Melanoma antigen recognized by T-cells 1C10Homo sapiensMutation(s): 1 
Gene Names: MLANAMART1
Find proteins for Q16655 (Homo sapiens)
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PHAROS  Q16655
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DMF5 T-cell Receptor Alpha Chain fusionD200Homo sapiensMutation(s): 2 
Gene Names: TRAV12-2
Find proteins for A0A075B6T6 (Homo sapiens)
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PHAROS  A0A075B6T6
Find proteins for P01848 (Homo sapiens)
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PHAROS  P01848
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DMF5 T-cell Receptor Beta Chain fusionE243Homo sapiensMutation(s): 0 
Gene Names: TRBV6-4
Find proteins for A0A1B0GXE1 (Homo sapiens)
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Find proteins for K7N5M4 (Homo sapiens)
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.485α = 90
b = 49.063β = 94.98
c = 92.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

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 States--

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence