6PBH

Crystal Structure of HLA-A*68:01 in complex with NP145-156, a 12 mer influenza peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Challenging immunodominance of influenza-specific CD8+T cell responses restricted by the risk-associated HLA-A*68:01 allomorph.

van de Sandt, C.E., Clemens, E.B., Grant, E.J., Rowntree, L.C., Sant, S., Halim, H., Crowe, J., Cheng, A.C., Kotsimbos, T.C., Richards, M., Miller, A., Tong, S.Y.C., Rossjohn, J., Nguyen, T.H.O., Gras, S., Chen, W., Kedzierska, K.

(2019) Nat Commun 10: 5579-5579

  • DOI: 10.1038/s41467-019-13346-4
  • Primary Citation of Related Structures:  
    6PBH

  • PubMed Abstract: 

    • Although influenza viruses lead to severe illness in high-risk populations, host genetic factors associated with severe disease are largely unknown. As the HLA-A*68:01 allele can be linked to severe pandemic 2009-H1N1 disease, we investigate a potent ...

    Although influenza viruses lead to severe illness in high-risk populations, host genetic factors associated with severe disease are largely unknown. As the HLA-A*68:01 allele can be linked to severe pandemic 2009-H1N1 disease, we investigate a potential impairment of HLA-A*68:01-restricted CD8 + T cells to mount robust responses. We elucidate the HLA-A*68:01 + CD8 + T cell response directed toward an extended influenza-derived nucleoprotein (NP) peptide and show that only ~35% individuals have immunodominant A68/NP 145 + CD8 + T cell responses. Dissecting A68/NP 145 + CD8 + T cells in low vs. medium/high responders reveals that high responding donors have A68/NP 145 + CD8 + memory T cells with clonally expanded TCRαβs, while low-responders display A68/NP 145 + CD8 + T cells with predominantly naïve phenotypes and non-expanded TCRαβs. Single-cell index sorting and TCRαβ analyses link expansion of A68/NP 145 + CD8 + T cells to their memory potential. Our study demonstrates the immunodominance potential of influenza-specific CD8 + T cells presented by a risk HLA-A*68:01 molecule and advocates for priming CD8 + T cell compartments in HLA-A*68:01-expressing individuals for establishment of pre-existing protective memory T cell pools.

    Organizational Affiliation: 

    Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute, Melbourne, VIC, 3000, Australia. kkedz@unimelb.edu.au.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-68 alpha chainA279Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
GTEx  ENSG00000206503
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
influenza A NP145-156 peptideC12unidentified influenza virusMutation(s): 0 
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Explore Q9Q0U8 
Go to UniProtKB:  Q9Q0U8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
SO4
Query on SO4
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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.75α = 90
b = 79.004β = 90
c = 112.651γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2019-06-13 
  • Released Date: 2019-12-11 
    • Deposition Author(s): Gras, S.

Revision History 

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references