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 6PBH | pdb_00006pbh

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 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6PBH

This is version 1.3 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: https://doi.org/10.1038/s41467-019-13346-4
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 45.83 kDa 
  • Atom Count: 3,458 
  • Modeled Residue Count: 378 
  • Deposited Residue Count: 390 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-68 alpha chain279Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
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UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
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UniProt GroupP61769
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
influenza A NP145-156 peptide12unidentified influenza virusMutation(s): 0 
UniProt
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd))
Explore Q9Q0U8 
Go to UniProtKB:  Q9Q0U8
Entity Groups
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UniProt GroupQ9Q0U8
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.234 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
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

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary