5JHD

Crystal structure of LS10-TCR/M1-HLA-A*02 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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This is version 1.5 of the entry. See complete history. 


Literature

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8(+) T cell epitope.

Song, I., Gil, A., Mishra, R., Ghersi, D., Selin, L.K., Stern, L.J.

(2017) Nat Struct Mol Biol 24: 395-406

  • DOI: https://doi.org/10.1038/nsmb.3383
  • Primary Citation of Related Structures:  
    5ISZ, 5JHD

  • PubMed Abstract: 

    • A keystone of antiviral immunity is CD8 + T cell recognition of viral peptides bound to MHC-I proteins. The recognition modes of individual T cell receptors (TCRs) have been studied in some detail, but the role of TCR variation in providing a robust response to viral antigens is unclear ...

    A keystone of antiviral immunity is CD8 + T cell recognition of viral peptides bound to MHC-I proteins. The recognition modes of individual T cell receptors (TCRs) have been studied in some detail, but the role of TCR variation in providing a robust response to viral antigens is unclear. The influenza M1 epitope is an immunodominant target of CD8 + T cells that help to control influenza in HLA-A2 + individuals. Here we show that CD8 + T cells use many distinct TCRs to recognize HLA-A2-M1, which enables the use of different structural solutions to the problem of specifically recognizing a relatively featureless peptide antigen. The vast majority of responding TCRs target a small cleft between HLA-A2 and the bound M1 peptide. These broad repertoires lead to plasticity in antigen recognition and protection against T cell clonal loss and viral escape.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain
A, F
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
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UniProt GroupP04439
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
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PHAROS:  P61769
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UniProt GroupP61769
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Influenza M1(58-66) peptide
C, H
9Influenza A virusMutation(s): 0 
UniProt
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03485 
Go to UniProtKB:  P03485
Entity Groups  
UniProt GroupP03485
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
TCRalpha chain
D, I
213Homo sapiensMutation(s): 0 
Gene Names: TRA@
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
TCRbeta chain
E, J
242Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDT
Query on EDT
Download Ideal Coordinates CCD File 
K [auth E],
L [auth J]		{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.71α = 99.38
b = 101.84β = 92.6
c = 113.55γ = 103.45
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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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 StatesAI038996
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI109858
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI49320

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence