6Z6W | pdb_00006z6w

Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) from a mammalian expression system.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Z6W

This is version 1.4 of the entry. See complete history

Literature

Mammalian expression of virus-like particles as a proof of principle for next generation polio vaccines.

Bahar, M.W.Porta, C.Fox, H.Macadam, A.J.Fry, E.E.Stuart, D.I.

(2021) NPJ Vaccines 6: 5-5

  • DOI: https://doi.org/10.1038/s41541-020-00267-3
  • Primary Citation Related Structures: 
    6Z6W

  • PubMed Abstract: 

    Global vaccination programs using live-attenuated oral and inactivated polio vaccine (OPV and IPV) have almost eradicated poliovirus (PV) but these vaccines or their production pose significant risk in a polio-free world. Recombinant PV virus-like particles (VLPs), lacking the viral genome, represent safe next-generation vaccines, however their production requires optimisation. Here we present an efficient mammalian expression strategy producing good yields of wild-type PV VLPs for all three serotypes and a thermostabilised variant for PV3. Whilst the wild-type VLPs were predominantly in the non-native C-antigenic form, the thermostabilised PV3 VLPs adopted the native D-antigenic conformation eliciting neutralising antibody titres equivalent to the current IPV and were indistinguishable from natural empty particles by cryo-electron microscopy with a similar stabilising lipidic pocket-factor in the VP1 β-barrel. This factor may not be available in alternative expression systems, which may require synthetic pocket-binding factors. VLPs equivalent to these mammalian expressed thermostabilized particles, represent safer non-infectious vaccine candidates for the post-eradication era.


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

Macromolecule Content 

  • Total Structure Weight: 97.8 kDa 
  • Atom Count: 5,646 
  • Modeled Residue Count: 713 
  • Deposited Residue Count: 878 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteins, VP1A [auth 1]300Poliovirus 3Mutation(s): 2 
UniProt
Find proteins for Q84895 (Poliovirus 3)
Explore Q84895 
Go to UniProtKB:  Q84895
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84895
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteins, VP0B [auth 0]340Poliovirus 3Mutation(s): 4 
UniProt
Find proteins for P03302 (Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B))
Explore P03302 
Go to UniProtKB:  P03302
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03302
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid proteins, VP3C [auth 3]238Poliovirus 3Mutation(s): 2 
UniProt
Find proteins for P03302 (Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B))
Explore P03302 
Go to UniProtKB:  P03302
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03302
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPH

Query on SPH



Download:Ideal Coordinates CCD File
D [auth 1]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev-3699
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references, Structure summary
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 1.3: 2022-09-21
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2024-07-10
    Changes: Data collection, Refinement description