4JFP

A2 HLA complex with G4A heteroclitic variant of Melanoma peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

T-cell receptor specificity maintained by altered thermodynamics.

Madura, F.Rizkallah, P.J.Miles, K.M.Holland, C.J.Bulek, A.M.Fuller, A.Schauenburg, A.J.Miles, J.J.Liddy, N.Sami, M.Li, Y.Hossain, M.Baker, B.M.Jakobsen, B.K.Sewell, A.K.Cole, D.K.

(2013) J.Biol.Chem. 288: 18766-18775

  • DOI: 10.1074/jbc.M113.464560
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The T-cell receptor (TCR) recognizes peptides bound to major histocompatibility molecules (MHC) and allows T-cells to interrogate the cellular proteome for internal anomalies from the cell surface. The TCR contacts both MHC and peptide in an interact ...

    The T-cell receptor (TCR) recognizes peptides bound to major histocompatibility molecules (MHC) and allows T-cells to interrogate the cellular proteome for internal anomalies from the cell surface. The TCR contacts both MHC and peptide in an interaction characterized by weak affinity (KD = 100 nM to 270 μM). We used phage-display to produce a melanoma-specific TCR (α24β17) with a 30,000-fold enhanced binding affinity (KD = 0.6 nM) to aid our exploration of the molecular mechanisms utilized to maintain peptide specificity. Remarkably, although the enhanced affinity was mediated primarily through new TCR-MHC contacts, α24β17 remained acutely sensitive to modifications at every position along the peptide backbone, mimicking the specificity of the wild type TCR. Thermodynamic analyses revealed an important role for solvation in directing peptide specificity. These findings advance our understanding of the molecular mechanisms that can govern the exquisite peptide specificity characteristic of TCR recognition.


    Organizational Affiliation

    Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A, D
276Homo 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, E
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
G4A heteroclitic Melanoma peptide
C, F
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, D, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 202.590α = 90.00
b = 49.110β = 123.02
c = 117.600γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
SCALAdata scaling
GDAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2013-07-17
    Type: Database references