4JFH | pdb_00004jfh

High Affinity alpha24-beta17 T Cell Receptor for A2 HLA-Melanoma peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.247 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4JFH

This is version 1.4 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 Biological Chem 288: 18766-18775

  • DOI: https://doi.org/10.1074/jbc.M113.464560
  • Primary Citation Related Structures: 
    4JFD, 4JFE, 4JFF, 4JFH, 4JFO, 4JFP, 4JFQ

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 50.25 kDa 
  • Atom Count: 3,694 
  • Modeled Residue Count: 444 
  • Deposited Residue Count: 444 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
alpha24 TCR alleleA [auth D]200Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01848 (Homo sapiens)
Explore P01848 
Go to UniProtKB:  P01848
PHAROS:  P01848
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01848
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
beta17 TCR alleleB [auth E]244Homo sapiensMutation(s): 0 
UniProt
Find proteins for P01850 (Homo sapiens)
Explore P01850 
Go to UniProtKB:  P01850
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01850
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth D],
J [auth E],
K [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
G [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth D],
D,
E [auth D],
F [auth D],
I [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.247 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.14α = 90
b = 97.14β = 90
c = 123.08γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection
xia2data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2013-06-19
    Changes: Database references
  • Version 1.3: 2013-07-17
    Changes: Database references
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary