8PJG

F11 TCR in complex with Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P4GClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4 + T cell activation.

Hulin-Curtis, S.Geary, J.K.MacLachlan, B.J.Altmann, D.M.Baillon, L.Cole, D.K.Greenshields-Watson, A.Hesketh, S.J.Humphreys, I.R.Jones, I.M.Lauder, S.N.Mason, G.H.Smart, K.Scourfield, D.O.Scott, J.Sukhova, K.Stanton, R.J.Wall, A.Rizkallah, P.J.Barclay, W.S.Gallimore, A.Godkin, A.

(2024) Cell Rep 43: 114259-114259

  • DOI: https://doi.org/10.1016/j.celrep.2024.114259
  • Primary Citation of Related Structures:  
    8PJE, 8PJF, 8PJG

  • PubMed Abstract: 

    CD4 + T cells are central to adaptive immunity. Their role in cross-protection in viral infections such as influenza and severe acute respiratory syndrome (SARS) is well documented; however, molecular rules governing T cell receptor (TCR) engagement of peptide-human leukocyte antigen (pHLA) class II are less understood. Here, we exploit an aspect of HLA class II presentation, the peptide-flanking residues (PFRs), to "tune" CD4 + T cell responses within an in vivo model system of influenza. Using a recombinant virus containing targeted substitutions at immunodominant HLA-DR1 epitopes, we demonstrate limited weight loss and improved clinical scores after heterosubtypic re-challenge. We observe enhanced protection linked to lung-derived influenza-specific CD4 + and CD8 + T cells prior to re-infection. Structural analysis of the ternary TCR:pHLA complex identifies that flanking amino acids influence side chains in the core 9-mer peptide, increasing TCR affinity. Augmentation of CD4 + T cell immunity is achievable with a single mutation, representing a strategy to enhance adaptive immunity that is decoupled from vaccine modality.


  • Organizational Affiliation

    Division of Infection and Immunity/Systems Immunity University Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain183Homo sapiensMutation(s): 0 
Gene Names: HLA-DRAHLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
PHAROS:  P01903
GTEx:  ENSG00000204287 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01903
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1 beta chain191Homo sapiensMutation(s): 13 
Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
Explore P01911 
Go to UniProtKB:  P01911
PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain13Influenza A virusMutation(s): 1 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Explore P03437 
Go to UniProtKB:  P03437
Entity Groups  
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UniProt GroupP03437
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha chain constant207Homo sapiensMutation(s): 0 
Gene Names: TRACTCRA
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor beta constant 1241Homo sapiensMutation(s): 0 
Gene Names: TRBC1
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4G
Query on P4G

Download Ideal Coordinates CCD File 
N [auth D],
V [auth E]
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth C]
I [auth D]
J [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.61α = 90
b = 184.82β = 90
c = 50.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted P4GClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom209213/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary