3QDM

The complex between TCR DMF4 and human Class I MHC HLA-A2 with the bound MART-1(26-35)(A27L) decameric peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

TCRs Used in Cancer Gene Therapy Cross-React with MART-1/Melan-A Tumor Antigens via Distinct Mechanisms.

Borbulevych, O.Y.Santhanagopolan, S.M.Hossain, M.Baker, B.M.

(2011) J.Immunol. 187: 2453-2463

  • DOI: 10.4049/jimmunol.1101268
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • T cells engineered to express TCRs specific for tumor Ags can drive cancer regression. The first TCRs used in cancer gene therapy, DMF4 and DMF5, recognize two structurally distinct peptide epitopes of the melanoma-associated MART-1/Melan-A protein, ...

    T cells engineered to express TCRs specific for tumor Ags can drive cancer regression. The first TCRs used in cancer gene therapy, DMF4 and DMF5, recognize two structurally distinct peptide epitopes of the melanoma-associated MART-1/Melan-A protein, both presented by the class I MHC protein HLA-A*0201. To help understand the mechanisms of TCR cross-reactivity and provide a foundation for the further development of immunotherapy, we determined the crystallographic structures of DMF4 and DMF5 in complex with both of the MART-1/Melan-A epitopes. The two TCRs use different mechanisms to accommodate the two ligands. Although DMF4 binds the two with a different orientation, altering its position over the peptide/MHC, DMF5 binds them both identically. The simpler mode of cross-reactivity by DMF5 is associated with higher affinity toward both ligands, consistent with the superior functional avidity of DMF5. More generally, the observation of two diverging mechanisms of cross-reactivity with the same Ags and the finding that TCR-binding orientation can be determined by peptide alone extend our understanding of the mechanisms underlying TCR cross-reactivity.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A
275Homo 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
MART-1(27-35) 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
DMF4 alpha chain
D
195Homo sapiensMutation(s): 0 
Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens)
Go to UniProtKB:  P01848
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DMF4 beta chain
E
242N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.012α = 90.00
b = 69.745β = 90.00
c = 227.103γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-17
    Type: Database references
  • Version 1.3: 2011-09-07
    Type: Database references