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 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
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UniProt GroupP03437
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  • Reference Sequence
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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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  • Reference Sequence
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]
F [auth B],
G [auth B],
H [auth C],
I [auth D],
J [auth D],
K [auth D],
L [auth D],
M [auth D],
O [auth E],
P [auth E],
Q [auth E],
R [auth E],
S [auth E],
T [auth E],
U [auth E]
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 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • 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 


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