8AYZ

Poliovirus type 2 (strain MEF-1) virus-like particle in complex with capsid binder compound 17


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A conserved glutathione binding site in poliovirus is a target for antivirals and vaccine stabilisation.

Bahar, M.W.Nasta, V.Fox, H.Sherry, L.Grehan, K.Porta, C.Macadam, A.J.Stonehouse, N.J.Rowlands, D.J.Fry, E.E.Stuart, D.I.

(2022) Commun Biol 5: 1293-1293

  • DOI: https://doi.org/10.1038/s42003-022-04252-5
  • Primary Citation of Related Structures:  
    8AYX, 8AYY, 8AYZ

  • PubMed Abstract: 

    Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or attenuated virus vaccines, instability of VLPs can compromise their immunogenicity. Glutathione (GSH), an important cellular reducing agent, is a crucial co-factor for the morphogenesis of enteroviruses, including PV. We report cryo-EM structures of GSH bound to PV serotype 3 VLPs showing that it can enhance particle stability. GSH binds the positively charged pocket at the interprotomer interface shown recently to bind GSH in enterovirus F3 and putative antiviral benzene sulphonamide compounds in other enteroviruses. We show, using high-resolution cryo-EM, the binding of a benzene sulphonamide compound with a PV serotype 2 VLP, consistent with antiviral activity through over-stabilizing the interprotomer pocket, preventing the capsid rearrangements necessary for viral infection. Collectively, these results suggest GSH or an analogous tight-binding antiviral offers the potential for stabilizing VLP vaccines.


  • Organizational Affiliation

    Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK. mohammad.bahar@strubi.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein, VP1301Poliovirus 2Mutation(s): 1 
UniProt
Find proteins for P06210 (Poliovirus type 2 (strain Lansing))
Explore P06210 
Go to UniProtKB:  P06210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06210
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein, VP0340Poliovirus 2Mutation(s): 0 
UniProt
Find proteins for P06210 (Poliovirus type 2 (strain Lansing))
Explore P06210 
Go to UniProtKB:  P06210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06210
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein, VP3238Poliovirus 2Mutation(s): 0 
UniProt
Find proteins for P06210 (Poliovirus type 2 (strain Lansing))
Explore P06210 
Go to UniProtKB:  P06210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06210
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FHK (Subject of Investigation/LOI)
Query on FHK

Download Ideal Coordinates CCD File 
E [auth A]4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid
C21 H14 N2 O6 S
KCHARURJHJMOQX-UHFFFAOYSA-N
SPH
Query on SPH

Download Ideal Coordinates CCD File 
D [auth A]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.1
MODEL REFINEMENTPHENIX1.19.2-4158-000

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesRG.IMCB.I8-TSA-083

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release