4QOK

Structural basis for ineffective T-cell responses to MHC anchor residue improved heteroclitic peptides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides.

Madura, F.Rizkallah, P.J.Holland, C.J.Fuller, A.Bulek, A.Godkin, A.J.Schauenburg, A.J.Cole, D.K.Sewell, A.K.

(2015) Eur.J.Immunol. 45: 584-591

  • DOI: 10.1002/eji.201445114

  • PubMed Abstract: 
  • MHC anchor residue-modified "heteroclitic" peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26-35 peptide, EAAGIGI ...

    MHC anchor residue-modified "heteroclitic" peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26-35 peptide, EAAGIGILTV, where the natural alanine at position 2 has been modified to leucine to improve human leukocyte antigen (HLA)-A*0201 anchoring. The resulting ELAGIGILTV peptide has been used in many studies. We recently showed that T cells primed with the ELAGIGILTV peptide can fail to recognize the natural tumor-expressed peptide efficiently, thereby providing a potential molecular reason for why clinical trials of this peptide have been unsuccessful. Here, we solved the structure of a TCR in complex with HLA-A*0201-EAAGIGILTV peptide and compared it with its heteroclitic counterpart , HLA-A*0201-ELAGIGILTV. The data demonstrate that a suboptimal anchor residue at position 2 enables the TCR to "pull" the peptide away from the MHC binding groove, facilitating extra contacts with both the peptide and MHC surface. These data explain how a TCR can distinguish between two epitopes that differ by only a single MHC anchor residue and demonstrate how weak MHC anchoring can enable an induced-fit interaction with the TCR. Our findings constitute a novel demonstration of the extreme sensitivity of the TCR to minor alterations in peptide conformation.


    Organizational Affiliation

    Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A
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
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
Melanoma antigen recognized by T-cells 1 marker peptide
C
10Homo sapiensMutation(s): 0 
Gene Names: MLANA (MART1)
Find proteins for Q16655 (Homo sapiens)
Go to Gene View: MLANA
Go to UniProtKB:  Q16655
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mel5 TCR chain alpha
D
194N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Mel5 TCR chain beta
E
244N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, 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: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.203 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 120.690α = 90.00
b = 120.690β = 90.00
c = 82.060γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
GDAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description