7RTR | pdb_00007rtr

YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.235 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Molecular Basis of a Dominant SARS-CoV-2 Spike-Derived Epitope Presented by HLA-A*02:01 Recognised by a Public TCR.

Szeto, C.Nguyen, A.T.Lobos, C.A.Chatzileontiadou, D.S.M.Jayasinghe, D.Grant, E.J.Riboldi-Tunnicliffe, A.Smith, C.Gras, S.

(2021) Cells 10

  • DOI: https://doi.org/10.3390/cells10102646
  • Primary Citation Related Structures: 
    7RTD, 7RTR

  • PubMed Abstract: 

    The data currently available on how the immune system recognises the SARS-CoV-2 virus is growing rapidly. While there are structures of some SARS-CoV-2 proteins in complex with antibodies, which helps us understand how the immune system is able to recognise this new virus; however, we lack data on how T cells are able to recognise this virus. T cells, especially the cytotoxic CD8+ T cells, are critical for viral recognition and clearance. Here we report the X-ray crystallography structure of a T cell receptor, shared among unrelated individuals (public TCR) in complex with a dominant spike-derived CD8+ T cell epitope (YLQ peptide). We show that YLQ activates a polyfunctional CD8+ T cell response in COVID-19 recovered patients. We detail the molecular basis for the shared TCR gene usage observed in HLA-A*02:01+ individuals, providing an understanding of TCR recognition towards a SARS-CoV-2 epitope. Interestingly, the YLQ peptide conformation did not change upon TCR binding, facilitating the high-affinity interaction observed.


  • Organizational Affiliation
    • Viral and Structural Immunology Laboratory, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, School of Molecular Sciences, La Trobe University, Bundoora, VIC 3086, Australia.

Macromolecule Content 

  • Total Structure Weight: 104.38 kDa 
  • Atom Count: 6,644 
  • Modeled Residue Count: 811 
  • Deposited Residue Count: 918 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I antigen365Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLA
UniProt
Find proteins for Q53Z42 (Homo sapiens)
Explore Q53Z42 
Go to UniProtKB:  Q53Z42
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53Z42
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
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 GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S19Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
UniProt GroupP0DTC2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
YLQ-SG3 TCR alpha chain (TRAV12-2)203Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
YLQ-SG3 TCR beta chain (TRBV7-9)241Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.235 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.356α = 90
b = 49.622β = 91.83
c = 91.725γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary