4GRM | pdb_00004grm

The crystal structure of the high affinity TCR A6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.295 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4GRM

This is version 1.2 of the entry. See complete history

Literature

Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode.

Cole, D.K.Sami, M.Scott, D.R.Rizkallah, P.J.Borbulevych, O.Y.Todorov, P.T.Moysey, R.K.Jakobsen, B.K.Boulter, J.M.Baker, B.M.Li, Y.I.

(2013) Front Immunol 4: 168-168

  • DOI: https://doi.org/10.3389/fimmu.2013.00168
  • Primary Citation Related Structures: 
    4GRM

  • PubMed Abstract: 

    Natural T cell receptors (TCRs) generally bind to their cognate pMHC molecules with weak affinity and fast kinetics, limiting their use as therapeutic agents. Using phage display, we have engineered a high affinity version of the A6 wild-type TCR (A6wt), specific for the human leukocyte antigen (HLA-A(∗)0201) complexed with human T cell lymphotropic virus type 111-19 peptide (A2-Tax). Mutations in just 4 residues in the CDR3β loop region of the A6wt TCR were selected that improved binding to A2-Tax by nearly 1000-fold. Biophysical measurements of this mutant TCR (A6c134) demonstrated that the enhanced binding was derived through favorable enthalpy and a slower off-rate. The structure of the free A6c134 TCR and the A6c134/A2-Tax complex revealed a native binding mode, similar to the A6wt/A2-Tax complex. However, concordant with the more favorable binding enthalpy, the A6c134 TCR made increased contacts with the Tax peptide compared with the A6wt/A2-Tax complex, demonstrating a peptide-focused mechanism for the enhanced affinity that directly involved the mutated residues in the A6c134 TCR CDR3β loop. This peptide-focused enhanced TCR binding may represent an important approach for developing antigen specific high affinity TCR reagents for use in T cell based therapies.


  • Organizational Affiliation
    • Cardiff University School of Medicine, Heath Park , Cardiff , UK.

Macromolecule Content 

  • Total Structure Weight: 97.7 kDa 
  • Atom Count: 6,612 
  • Modeled Residue Count: 854 
  • Deposited Residue Count: 878 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
A6 alpha chain
A, C
194Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
A6 beta chain
B, D
245Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.295 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.491α = 90
b = 51.969β = 104.94
c = 95.218γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Structure summary