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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-68 alpha chainA279Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
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: B2MCDABP0092HDCMA22P
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
  • Find similar proteins by:  Sequence   |   Structure
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

Download CCD File 
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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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