2JCC

AH3 recognition of mutant HLA-A2 W167A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Single Mhc Mutation Eliminates Enthalpy Associated with T Cell Receptor Binding.

Miller, P.Pazy, Y.Conti, B.Riddle, D.Appella, E.Collins, E.J.

(2007) J.Mol.Biol. 373: 315

  • DOI: 10.1016/j.jmb.2007.07.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The keystone of the adaptive immune response is T cell receptor (TCR) recognition of peptide presented by major histocompatibility complex (pMHC) molecules. The crystal structure of AHIII TCR bound to MHC, HLA-A2, showed a large interface with an aty ...

    The keystone of the adaptive immune response is T cell receptor (TCR) recognition of peptide presented by major histocompatibility complex (pMHC) molecules. The crystal structure of AHIII TCR bound to MHC, HLA-A2, showed a large interface with an atypical binding orientation. MHC mutations in the interface of the proteins were tested for changes in TCR recognition. From the range of responses observed, three representative HLA-A2 mutants, T163A, W167A, and K66A, were selected for further study. Binding constants and co-crystal structures of the AHIII TCR and the three mutants were determined. K66 in HLA-A2 makes contacts with both peptide and TCR, and has been identified as a critical residue for recognition by numerous TCR. The K66A mutation resulted in the lowest AHIII T cell response and the lowest binding affinity, which suggests that the T cell response may correlate with affinity. Importantly, the K66A mutation does not affect the conformation of the peptide. The change in affinity appears to be due to a loss in hydrogen bonds in the interface as a result of a conformational change in the TCR complementarity-determining region 3 (CDR3) loop. Isothermal titration calorimetry confirmed the loss of hydrogen bonding by a large loss in enthalpy. Our findings are inconsistent with the notion that the CDR1 and CDR2 loops of the TCR are responsible for MHC restriction, while the CDR3 loops interact solely with the peptide. Instead, we present here an MHC mutation that does not change the conformation of the peptide, yet results in an altered conformation of a CDR3.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN
A, H
275Homo sapiensMutation(s): 1 
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, I
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
P1049
C, J
9Homo sapiensMutation(s): 0 
Gene Names: EMC7 (C11orf3, C15orf24)
Find proteins for Q9NPA0 (Homo sapiens)
Go to Gene View: EMC7
Go to UniProtKB:  Q9NPA0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
TCR ALPHA
E, L
194Mus musculusMutation(s): 0 
Gene Names: Tcra
Find proteins for P01849 (Mus musculus)
Go to UniProtKB:  P01849
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
TCR BETA
F, M
238N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.280α = 90.00
b = 84.346β = 92.53
c = 122.470γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance