6D7G | pdb_00006d7g

Structure of 5F3 TCR in complex with HLA-A2/MART-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.237 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Generation and molecular recognition of melanoma-associated antigen-specific human gamma delta T cells.

Benveniste, P.M.Roy, S.Nakatsugawa, M.Chen, E.L.Y.Nguyen, L.Millar, D.G.Ohashi, P.S.Hirano, N.Adams, E.J.Zuniga-Pflucker, J.C.

(2018) Sci Immunol 3

  • DOI: https://doi.org/10.1126/sciimmunol.aav4036
  • Primary Citation of Related Structures:  
    6D7G

  • PubMed Abstract: 

    Antigen recognition by T cells bearing αβ T cell receptors (TCRs) is restricted by major histocompatibility complex (MHC). However, how antigens are recognized by T cells bearing γδ TCRs remains unclear. Although γδ T cells can recognize nonclassical MHC, it is generally thought that recognition of antigens is not MHC restricted. Here, we took advantage of an in vitro system to generate antigen-specific human T cells and show that melanoma-associated antigens, MART-1 and gp100, can be recognized by γδ T cells in an MHC-restricted fashion. Cloning and transferring of MART-1-specific γδ TCRs restored the specific recognition of the initial antigen MHC/peptide reactivity and conferred antigen-specific functional responses. A crystal structure of a MART-1-specific γδ TCR, together with MHC/peptide, revealed distinctive but similar docking properties to those previously reported for αβ TCRs, recognizing MART-1 on HLA-A*0201. Our work shows that antigen-specific and MHC-restricted γδ T cells can be generated in vitro and that MART-1-specific γδ T cells can also be found and cloned from the naïve repertoire. These findings reveal that classical MHC-restricted human γδ TCRs exist in the periphery and have the potential to be used in developing of new TCR-based immunotherapeutic approaches.


  • Organizational Affiliation

    Sunnybrook Research Institute, Toronto, ON, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA427Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP04439P61769
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRA@ proteinB [auth D]229Homo sapiensMutation(s): 0 
Gene Names: TRA@
UniProt
Find proteins for Q6PJ56 (Homo sapiens)
Explore Q6PJ56 
Go to UniProtKB:  Q6PJ56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PJ56
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGIONC [auth E]258Homo sapiensMutation(s): 0 
Gene Names: TRGV8TRGC2
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.953α = 90
b = 123.953β = 90
c = 154.156γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-10-23
    Changes: Data collection, Database references, Structure summary