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- PDB-9h93: Poliovirus type 2 (strain MEF-1) stabilised virus-like particle (... -

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Basic information

Entry
Database: PDB / ID: 9h93
TitlePoliovirus type 2 (strain MEF-1) stabilised virus-like particle (PV2 SC6b) from a yeast expression system.
Components
  • Capsid protein VP1
  • Capsid protein VP3
  • Capsid protein, VP0
KeywordsVIRUS LIKE PARTICLE / Capsid protein / virus-like particle / vaccine
Function / homology
Function and homology information


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 / receptor-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...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 / receptor-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsBahar, M.W. / 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: NPJ Vaccines / Year: 2025
Title: Production of an immunogenic trivalent poliovirus virus-like particle vaccine candidate in yeast using controlled fermentation.
Authors: Lee Sherry / Keith Grehan / Mohammad W Bahar / Jessica J Swanson / Helen Fox / Sue Matthews / Sarah Carlyle / Ling Qin / Claudine Porta / Steven Wilkinson / Suzanne Robb / Naomi Clark / John ...Authors: Lee Sherry / Keith Grehan / Mohammad W Bahar / Jessica J Swanson / Helen Fox / Sue Matthews / Sarah Carlyle / Ling Qin / Claudine Porta / Steven Wilkinson / Suzanne Robb / Naomi Clark / John Liddell / Elizabeth E Fry / David I Stuart / Andrew J Macadam / David J Rowlands / Nicola J Stonehouse /
Abstract: The success of the poliovirus (PV) vaccines has enabled the near-eradication of wild PV, however, their continued use post-eradication poses concerns, due to the potential for virus escape during ...The success of the poliovirus (PV) vaccines has enabled the near-eradication of wild PV, however, their continued use post-eradication poses concerns, due to the potential for virus escape during vaccine manufacture. Recombinant virus-like particles (VLPs) that lack the viral genome remove this risk. Here, we demonstrate the production of PV VLPs for all three serotypes by controlled fermentation using Pichia pastoris. We determined the cryo-EM structure of a new PV2 mutant, termed SC5a, in comparison to PV2-SC6b VLPs described previously and investigated the immunogenicity of PV2-SC5a VLPs. Finally, a trivalent immunogenicity trial using bioreactor-derived VLPs of all three serotypes in the presence of Alhydrogel adjuvant, showed that these VLPs outperform the current IPV vaccine in the standard vaccine potency assay, offering the potential for dose-sparing. Overall, these results provide further evidence that yeast-produced VLPs have the potential to be a next-generation polio vaccine in a post-eradication world.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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)97,2614
Polymers96,9613
Non-polymers2991
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)5,835,653240
Polymers5,817,683180
Non-polymers17,97060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein VP1 / Capsid protein VP1


Mass: 33105.246 Da / Num. of mol.: 1 / Mutation: VP1 V107I, VP1 F134L, VP1 V183L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus 2 / Strain: MEF-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q8QNU4
#2: Protein Capsid protein, VP0 / Capsid protein / VP0


Mass: 37398.816 Da / Num. of mol.: 1 / Mutation: VP4 I57V, VP2 D57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus 2 / Strain: MEF-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: P06210
#3: Protein Capsid protein VP3 / Capsid protein VP3


Mass: 26457.322 Da / Num. of mol.: 1 / Mutation: VP3 Q178L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus 2 / Strain: MEF-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A0K1U2R1
#4: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Poliovirus 2 / Type: VIRUS
Details: Recombinantly expressed virus-like particle of poliovirus type 2 (MEF-1 strain).
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 5.81 MDa / Experimental value: NO
Source (natural)Organism: Poliovirus 2 / Strain: MEF-1
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.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: 3ul of sample double 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: TFS KRIOS / Details: Calibrated pixel size was 0.831 A/pixel.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2300 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: 1.6 sec. / Electron dose: 35.12 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 29172
Details: Pixel sampling was 0.831 A/pixel. Energy filter was Gatan GIF Quantum.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selectionTemplate picker
2EPUimage acquisition
4cryoSPARC4.5.3CTF correctionPatch CTF
7UCSF Chimera1.16model fitting
8Coot0.9.6model fitting
10cryoSPARC4.5.3initial Euler assignmentab initio reconstruction
11cryoSPARC4.5.3final Euler assignmentHomogeneous reconstruction
12cryoSPARC4.5.3classificationHeterogeneous refinement
13cryoSPARC4.5.33D reconstructionHomogeneous reconstruction
14PHENIX1.20.1-4487-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 660747
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113853 / Algorithm: BACK PROJECTION
Details: Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -86.1 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: 1EAH

1eah


Accession code: 1EAH / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00333744
ELECTRON MICROSCOPYf_angle_d0.54645984
ELECTRON MICROSCOPYf_dihedral_angle_d12.07812150
ELECTRON MICROSCOPYf_chiral_restr0.0445064
ELECTRON MICROSCOPYf_plane_restr0.0045892

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