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- PDB-9f0k: Poliovirus type 1 (strain Mahoney) expanded conformation stabilis... -

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Basic information

Entry
Database: PDB / ID: 9f0k
TitlePoliovirus type 1 (strain Mahoney) expanded conformation stabilised virus-like particle (PV1 SC6b) from a mammalian expression system
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS LIKE PARTICLE / Capsid protein / 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 / 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 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 / 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 / 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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / 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
Biological speciesHuman poliovirus 1 Mahoney
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsBahar, M.W. / Porta, C. / 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 16, 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


Theoretical massNumber of molelcules
Total (without water)97,4643
Polymers97,4643
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP0
C: Capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,847,837180
Polymers5,847,837180
Non-polymers00
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: Mesocricetus auratus (golden hamster) / 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: Mesocricetus auratus (golden hamster) / 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: Mesocricetus auratus (golden hamster) / References: UniProt: P03300
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: all / Source: RECOMBINANT
Molecular weightValue: 5.84 MDa / Experimental value: NO
Source (natural)Organism: Human poliovirus 1 Mahoney / Strain: Mahoney
Source (recombinant)Organism: Mesocricetus auratus (golden hamster)
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.: 0.38 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample purified by sucrose density gradient ultracentrifugation.
Specimen supportDetails: The exact grid type was the ULtra-thin carbon support film, 3nm - on lacey carbon. Product code AGS187-4 from Agar Scientific.
Grid material: COPPER / 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 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: FEI TITAN KRIOS
Details: Preliminary grid screening was performed on a Glacios 200 kV microscope.
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: 1.27 sec. / Electron dose: 33.78 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5104 / Details: Pixel sampling was 1.08 A/pixel.
Image scansSampling size: 14 µm / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
4RELION3.0.7CTF correction
7UCSF Chimera1.16model fitting
8Coot0.9.6model fitting
10RELION3.0.7initial Euler assignment
11RELION3.0.7final Euler assignment
12RELION3.0.7classification
13RELION3.0.73D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionDetails: CTF correction performed in RELION v3.0.7 using CTFFIND4.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7185
Details: Particle picking was performed using crYOLO after training the neural network on approx. 100 manually picked particles.
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6252 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / 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_d0.00533300
ELECTRON MICROSCOPYf_angle_d0.52945354
ELECTRON MICROSCOPYf_dihedral_angle_d11.29512006
ELECTRON MICROSCOPYf_chiral_restr0.0455016
ELECTRON MICROSCOPYf_plane_restr0.0045784

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