8ROO | pdb_00008roo

Crystal structure of HLA B*18:01 in complex with YERMCNIL, an 8-mer epitope from Influenza A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.189 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.155 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Characterisation of novel influenza-derived HLA-B*18:01-restricted epitopes.

Leong, S.L.Murdolo, L.Maddumage, J.C.Koutsakos, M.Kedzierska, K.Purcell, A.W.Gras, S.Grant, E.J.

(2024) Clin Transl Immunology 13: e1509-e1509

  • DOI: https://doi.org/10.1002/cti2.1509
  • Primary Citation Related Structures: 
    8RNG, 8RNH, 8ROO, 8ROP

  • PubMed Abstract: 

    Seasonal influenza viruses cause roughly 650 000 deaths annually despite available vaccines. CD8 + T cells typically recognise influenza-derived peptides from internal structural and non-structural influenza proteins and are an attractive avenue for future vaccine design as they could reduce the severity of disease following infection with diverse influenza strains. CD8 + T cells recognise peptides presented by the highly polymorphic Human Leukocyte Antigens class I molecules (HLA-I). Each HLA-I variant has distinct peptide binding preferences, representing a significant obstacle for designing vaccines that elicit CD8 + T cell responses across broad populations. Consequently, the rational design of a CD8 + T cell-mediated vaccine would require the identification of highly immunogenic peptides restricted to a range of different HLA molecules. Here, we assessed the immunogenicity of six recently published novel influenza-derived peptides identified by mass-spectrometry and predicted to bind to the prevalent HLA-B*18:01 molecule. Using CD8 + T cell activation assays and protein biochemistry, we showed that 3/6 of the novel peptides were immunogenic in several HLA-B*18:01 + individuals and confirmed their HLA-B*18:01 restriction. We subsequently compared CD8 + T cell responses towards the previously identified highly immunogenic HLA-B*18:01-restricted NP 219 peptide. Using X-ray crystallography, we solved the first crystal structures of HLA-B*18:01 presenting immunogenic influenza-derived peptides. Finally, we dissected the first TCR repertoires specific for HLA-B*18:01 restricted pathogen-derived peptides, identifying private and restricted repertoires against each of the four peptides. Overall the characterisation of these novel immunogenic peptides provides additional HLA-B*18:01-restricted vaccine targets derived from the Matrix protein 1 and potentially the non-structural protein and the RNA polymerase catalytic subunit of influenza viruses.


  • Organizational Affiliation
    • Infection and Immunity Program, La Trobe Institute for Molecular Science (LIMS) La Trobe University Bundoora VIC Australia.

Macromolecule Content 

  • Total Structure Weight: 45.53 kDa 
  • Atom Count: 3,594 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 384 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigen276Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for S6AU73 (Homo sapiens)
Explore S6AU73 
Go to UniProtKB:  S6AU73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS6AU73
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Influenza A derived peptide/Nucleoprotein8Influenza A virus (A/X-31(H3N2))Mutation(s): 0 
UniProt
Find proteins for Q91UL1 (Influenza A virus (strain A/X-31 H3N2))
Explore Q91UL1 
Go to UniProtKB:  Q91UL1
Entity Groups
UniProt GroupQ91UL1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo 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

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
M [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth C],
O [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
(Subject of Investigation/LOI)

Query on NO3



Download:Ideal Coordinates CCD File
P [auth C]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
K
(Subject of Investigation/LOI)

Query on K



Download:Ideal Coordinates CCD File
L [auth A],
Q [auth C],
R [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.189 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.155 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.853α = 90
b = 81.482β = 90
c = 111.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary