3E2H

Structure of the m67 high-affinity mutant of the 2C TCR in complex with Ld/QL9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Distinct CDR3 Conformations in TCRs Determine the Level of Cross-Reactivity for Diverse Antigens, but Not the Docking Orientation

Jones, L.L.Colf, L.A.Stone, J.D.Garcia, K.C.Kranz, D.M.

(2008) J.Immunol. 181: 6255-6264

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • T cells are known to cross-react with diverse peptide MHC Ags through their alphabeta TCR. To explore the basis of such cross-reactivity, we examined the 2C TCR that recognizes two structurally distinct ligands, SIY-K(b) and alloantigen QL9-L(d). In ...

    T cells are known to cross-react with diverse peptide MHC Ags through their alphabeta TCR. To explore the basis of such cross-reactivity, we examined the 2C TCR that recognizes two structurally distinct ligands, SIY-K(b) and alloantigen QL9-L(d). In this study we characterized the cross-reactivity of several high-affinity 2C TCR variants that contained mutations only in the CDR3alpha loop. Two of the TCR lost their ability to cross-react with the reciprocal ligand (SIY-K(b)), whereas another TCR (m67) maintained reactivity with both ligands. Crystal structures of four of the TCRs in complex with QL9-L(d) showed that CDR1, CDR2, and CDR3beta conformations and docking orientations were remarkably similar. Although the CDR3alpha loop of TCR m67 conferred a 2000-fold higher affinity for SIY-K(b), the TCR maintained the same docking angle on QL9-L(d) as the 2C TCR. Thus, CDR3alpha dictated the affinity and level of cross-reactivity, yet it did so without affecting the conserved docking orientation.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, L-D alpha chain
A
175Mus musculusMutation(s): 9 
Gene Names: H2-L
Find proteins for P01897 (Mus musculus)
Go to UniProtKB:  P01897
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
QL9 PEPTIDE
Q
9Mus musculusMutation(s): 0 
Gene Names: Ogdh (Kiaa4192)
EC: 1.2.4.2
Find proteins for Q60597 (Mus musculus)
Go to UniProtKB:  Q60597
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T-cell receptor alpha chain V region PHDS58
B
109Mus musculusMutation(s): 7 
Find proteins for P01738 (Mus musculus)
Go to UniProtKB:  P01738
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
M67 TCR beta chain
C
110Mus musculusMutation(s): 0 
Find proteins for A2NTY6 (Mus musculus)
Go to UniProtKB:  A2NTY6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.223 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 112.603α = 90.00
b = 112.603β = 90.00
c = 272.451γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-18
    Type: Derived calculations
  • Version 1.3: 2017-10-25
    Type: Refinement description