3ERY

Different thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Different thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors

Jones, L.L.Colf, L.A.Bankovich, A.J.Stone, J.D.Gao, Y.G.Chan, C.M.Huang, R.H.Garcia, K.C.Kranz, D.M.

(2008) Biochemistry 47: 12398-12408

  • DOI: 10.1021/bi801349g

  • PubMed Abstract: 
  • To understand the mechanisms that govern T cell receptor (TCR)-peptide MHC (pMHC) binding and the role that different regions of the TCR play in affinity and antigen specificity, we have studied the TCR from T cell clone 2C. High-affinity mutants of ...

    To understand the mechanisms that govern T cell receptor (TCR)-peptide MHC (pMHC) binding and the role that different regions of the TCR play in affinity and antigen specificity, we have studied the TCR from T cell clone 2C. High-affinity mutants of the 2C TCR that bind QL9-L(d) as a strong agonist were generated previously by site-directed mutagenesis of complementarity determining regions (CDRs) 1beta, 2alpha, 3alpha, or 3beta. We performed isothermal titration calorimetry to assess whether they use similar thermodynamic mechanisms to achieve high affinity for QL9-L(d). Four of the five TCRs examined bound to QL9-L(d) in an enthalpically driven, entropically unfavorable manner. In contrast, the high-affinity CDR1beta mutant resembled the wild-type 2C TCR interaction, with favorable entropy. To assess fine specificity, we measured the binding and kinetics of these mutants for both QL9-L(d) and a single amino acid peptide variant of QL9, called QL9-Y5-L(d). While 2C and most of the mutants had equal or higher affinity for the Y5 variant than for QL9, mutant CDR1beta exhibited 8-fold lower affinity for Y5 compared to QL9. To examine possible structural correlates of the thermodynamic and fine specificity signatures of the TCRs, the structure of unliganded QL9-L(d) was solved and compared to structures of the 2C TCR/QL9-L(d) complex and three high-affinity TCR/QL9-L(d) complexes. Our findings show that the QL9-L(d) complex does not undergo major conformational changes upon binding. Thus, subtle changes in individual CDRs account for the diverse thermodynamic and kinetic binding mechanisms and for the different peptide fine specificities.


    Organizational Affiliation

    Department of Biochemistry and School of Chemical Sciences Biocrystallization Service, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen
A, B
174Mus musculusMutation(s): 0 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Go to UniProtKB:  P01897
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2-oxoglutarate dehydrogenase E1 peptide
P, Q
9Homo sapiensMutation(s): 0 
Gene Names: OGDH
EC: 1.2.4.2
Find proteins for Q02218 (Homo sapiens)
Go to Gene View: OGDH
Go to UniProtKB:  Q02218
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.163α = 90.00
b = 74.323β = 107.65
c = 53.255γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance