Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93346.43 
• Atom Count: 6576 
• Residue Count: 821 
• Unique protein chains: 5

3QEQ

The complex between TCR DMF4 and human Class I MHC HLA-A2 with the bound MART-1(27-35) nonameric peptide

• DOI: 10.2210/pdb3QEQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-01-20 Released: 2011-07-06 
• Deposition Author(s): Borbulevych, O.Y., Baker, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.269 
• R-Value Work: 0.215 

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

• PubMed: 21795600 
• DOI: 10.4049/jimmunol.1101268
• Primary Citation of Related Structures:  
  3QEU, 3QDM, 3QDJ, 3QDG


• 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, 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
HLA class I histocompatibility antigen, A-2 alpha chain	A	275	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M
Find proteins for P61769 (Homo sapiens) Go to Gene View: B2M Go to UniProtKB:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MART-1(27-35) peptide	C	9	Homo sapiens	Mutation(s): 0  Gene Names: MLANA (MART1)
Find proteins for Q16655 (Homo sapiens) Go to Gene View: MLANA Go to UniProtKB:  Q16655

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
DMF4 alpha chain	D	194	Homo sapiens	Mutation(s): 0  Gene Names: TRAC (TCRA)
Find proteins for P01848 (Homo sapiens) Go to UniProtKB:  P01848

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
DMF4 beta chain	E	243	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.269 
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.651	α = 90.00
b = 73.663	β = 90.00
c = 225.292	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
HKL-2000	data reduction
CrystalClear	data collection
HKL-2000	data scaling
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-20 
• Released Date: 2011-07-06 
• Deposition Author(s): Borbulevych, O.Y., Baker, B.M.

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
• Version 1.4: 2017-11-08
  Type: Refinement description