4L3E

The complex between high affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC HLA-A2 with the bound MART-1(26-35)(A27L) peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.557 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computational design of the affinity and specificity of a therapeutic T cell receptor.

Pierce, B.G.Hellman, L.M.Hossain, M.Singh, N.K.Vander Kooi, C.W.Weng, Z.Baker, B.M.

(2014) PLOS COMPUT.BIOL. 10: e1003478-e1003478

  • DOI: 10.1371/journal.pcbi.1003478

  • PubMed Abstract: 
  • T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, ther ...

    T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.


    Organizational Affiliation

    Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A
275Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P01892
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Melanoma antigen recognized by T-cells 1
C
10Homo sapiensMutation(s): 1 
Gene Names: MLANA (MART1)
Find proteins for Q16655 (Homo sapiens)
Go to Gene View: MLANA
Go to UniProtKB:  Q16655
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DMF5 alpha chain
D
199N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DMF5 beta chain
E
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.557 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 227.040α = 90.00
b = 49.316β = 94.82
c = 92.894γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-05 
  • Released Date: 2014-06-11 
  • Deposition Author(s): Hellman, L.M.

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-08-27
    Type: Database references