7N1B

SARS-CoV-2 RLQ peptide binds to HLA-A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors.

Wu, D.Kolesnikov, A.Yin, R.Guest, J.D.Gowthaman, R.Shmelev, A.Serdyuk, Y.Dianov, D.V.Efimov, G.A.Pierce, B.G.Mariuzza, R.A.

(2022) Nat Commun 13: 19-19

  • DOI: https://doi.org/10.1038/s41467-021-27669-8
  • Primary Citation of Related Structures:  
    7N1A, 7N1B, 7N1C, 7N1D, 7N1E, 7N1F

  • PubMed Abstract: 

    T cells play a vital role in combatting SARS-CoV-2 and forming long-term memory responses. Whereas extensive structural information is available on neutralizing antibodies against SARS-CoV-2, such information on SARS-CoV-2-specific T-cell receptors (TCRs) bound to their peptide-MHC targets is lacking. Here we determine the structures of a public and a private TCR from COVID-19 convalescent patients in complex with HLA-A2 and two SARS-CoV-2 spike protein epitopes (YLQ and RLQ). The structures reveal the basis for selection of particular TRAV and TRBV germline genes by the public but not the private TCR, and for the ability of the TCRs to recognize natural variants of RLQ but not YLQ. Neither TCR recognizes homologous epitopes from human seasonal coronaviruses. By elucidating the mechanism for TCR recognition of an immunodominant yet variable epitope (YLQ) and a conserved but less commonly targeted epitope (RLQ), this study can inform prospective efforts to design vaccines to elicit pan-coronavirus immunity.


  • Organizational Affiliation

    W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen, A-2 alpha chain
A, D
275Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens)
Explore A0A140T913 
Go to UniProtKB:  A0A140T913
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140T913
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
100Homo 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 S2
C, F
9Severe 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.204α = 91.89
b = 49.259β = 92.39
c = 117.094γ = 118.59
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI129893
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM126299

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-08-18
    Changes: Database references
  • Version 2.0: 2021-09-22
    Type: Coordinate replacement
    Reason: Real space R-factor
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2022-02-02
    Changes: Database references
  • Version 2.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description