6D7G

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 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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

    Department of Immunology, University of Toronto, Toronto, ON, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MART1 PEPTIDE-BETA-2-MICROGLOBULIN-HLA-A*02 CHIMERA A427Homo sapiensMutation(s): 0 
Gene Names: HLA-AB2MCDABP0092HDCMA22PHLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS:  P04439
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS:  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRA@ protein D229Homo sapiensMutation(s): 0 
Gene Names: TRA@
Find proteins for Q6PJ56 (Homo sapiens)
Explore Q6PJ56 
Go to UniProtKB:  Q6PJ56
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
T-CELL RECEPTOR GAMMA VARIABLE 8,T-CELL RECEPTOR GAMMA-2 CHAIN C REGION E258Homo sapiensMutation(s): 0 
Gene Names: TRGV8TRGC2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • 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



Entry History 

Deposition Data

  • Deposited Date: 2018-04-24 
  • Released Date: 2019-01-23 
  • Deposition Author(s): Roy, S., Adams, E.J.

Revision History 

  • 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