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- PDB-9f3q: Poliovirus type 1 (strain Mahoney) stabilised virus-like particle... -

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Basic information

Entry
Database: PDB / ID: 9f3q
TitlePoliovirus type 1 (strain Mahoney) stabilised virus-like particle (PV1 SC6b) in complex with GPP3 and GSH.
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS LIKE PARTICLE / Capsid protein / virus-like particle / inhibitor / complex / vaccine
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GLUTATHIONE / Chem-YM2 / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1 Mahoney
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsBahar, M.W. / Nasta, V. / Sherry, L. / Stonehouse, N.J. / Rowlands, D.J. / Fry, E.E. / Stuart, D.I.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationRG.IMCB.I8-TSA-083 United States
CitationJournal: Nat Commun / Year: 2025
Title: Recombinant expression systems for production of stabilised virus-like particles as next-generation polio vaccines.
Authors: Lee Sherry / Mohammad W Bahar / Claudine Porta / Helen Fox / Keith Grehan / Veronica Nasta / Helen M E Duyvesteyn / Luigi De Colibus / Johanna Marsian / Inga Murdoch / Daniel Ponndorf / ...Authors: Lee Sherry / Mohammad W Bahar / Claudine Porta / Helen Fox / Keith Grehan / Veronica Nasta / Helen M E Duyvesteyn / Luigi De Colibus / Johanna Marsian / Inga Murdoch / Daniel Ponndorf / Seong-Ryong Kim / Sachin Shah / Sarah Carlyle / Jessica J Swanson / Sue Matthews / Clare Nicol / George P Lomonossoff / Andrew J Macadam / Elizabeth E Fry / David I Stuart / Nicola J Stonehouse / David J Rowlands /
Abstract: Polioviruses have caused crippling disease in humans for centuries, prior to the successful development of vaccines in the mid-1900's, which dramatically reduced disease prevalence. Continued use of ...Polioviruses have caused crippling disease in humans for centuries, prior to the successful development of vaccines in the mid-1900's, which dramatically reduced disease prevalence. Continued use of these vaccines, however, threatens ultimate disease eradication and achievement of a polio-free world. Virus-like particles (VLPs) that lack a viral genome represent a safer potential vaccine, although they require particle stabilization. Using our previously established genetic techniques to stabilize the structural capsid proteins, we demonstrate production of poliovirus VLPs of all three serotypes, from four different recombinant expression systems. We compare the antigenicity, thermostability and immunogenicity of these stabilized VLPs against the current inactivated polio vaccine, demonstrating equivalent or superior immunogenicity in female Wistar rats. Structural analyses of these recombinant VLPs provide a rational understanding of the stabilizing mutations and the role of potential excipients. Collectively, we have established these poliovirus stabilized VLPs as viable next-generation vaccine candidates for the future.
History
DepositionApr 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1825
Polymers97,4643
Non-polymers7182
Water00
1
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,890,907300
Polymers5,847,837180
Non-polymers43,070120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein VP1 / P1D / Virion protein 1


Mass: 33447.586 Da / Num. of mol.: 1 / Mutation: VP1 H248P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Production host: Komagataella pastoris (fungus) / References: UniProt: P03300
#2: Protein Capsid protein VP0 / VP4-VP2


Mass: 37465.812 Da / Num. of mol.: 1 / Mutation: VP2 T25A, VP2 D57E, VP4 R18G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Production host: Komagataella pastoris (fungus) / References: UniProt: P03300
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26550.549 Da / Num. of mol.: 1 / Mutation: VP3 L119M, VP3 Q178L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney / Production host: Komagataella pastoris (fungus) / References: UniProt: P03300
#4: Chemical ChemComp-YM2 / 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE


Mass: 410.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human poliovirus 1 Mahoney / Type: VIRUS
Details: Recombinantly expressed virus-like particle of poliovirus type 1 (Mahoney strain).
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 5.84 MDa / Experimental value: NO
Source (natural)Organism: Human poliovirus 1 Mahoney / Strain: Mahoney
Source (recombinant)Organism: Komagataella pastoris (fungus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Virus shell 1 / Diameter: 310 nm / Triangulation number (T number): 1
Buffer solutionpH: 7 / Details: 1 x DPBS, 20 mM EDTA, pH 7.0
Buffer component
IDConc.NameBuffer-ID
11 xDPBS1
220 mMEDTA1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample purified by sucrose density gradient ultracentrifugation. Concentrated sample mixed with GPP3 and GSH (10mM final) to form complex.
Specimen supportDetails: The exact grid type used was Ultra-thin carbon support film, 3nm - on lacey carbon (product AGS187-4, Agar Scientific).
Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: 3-4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Calibrated pixel size was 1.08 A/pix.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal magnification: 75000 X / Calibrated magnification: 129629 X / Nominal defocus max: 2900 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.77 sec. / Electron dose: 35.49 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4467
Details: Pixel sampling was 1.08 A/pixel. Images collected in linear mode on Falcon 3.
Image scansSampling size: 14 µm / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
4cryoSPARC4.2.1CTF correction
7UCSF Chimera1.16model fitting
8Coot0.9.6model fitting
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 159830
Details: Particle picking performed in cryoSPARC using the blob picker.
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23721 / Algorithm: BACK PROJECTION
Details: Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -146.7 Angstrom squared.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using phenix_real.space.refine.
Atomic model buildingPDB-ID: 1HXS

1hxs


Accession code: 1HXS / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338970
ELECTRON MICROSCOPYf_angle_d0.53953196
ELECTRON MICROSCOPYf_dihedral_angle_d11.314178
ELECTRON MICROSCOPYf_chiral_restr0.0465952
ELECTRON MICROSCOPYf_plane_restr0.0056966

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