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Yorodumi- PDB-5o5b: Poliovirus type 3 (strain Saukett) stabilized virus-like particle -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o5b | |||||||||
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Title | Poliovirus type 3 (strain Saukett) stabilized virus-like particle | |||||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Poliovirus / virus-like particle / vaccine | |||||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / 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 / picornain 2A / protein complex oligomerization / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C ...caveolin-mediated endocytosis of virus by host cell / 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 / picornain 2A / protein complex oligomerization / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / monoatomic ion channel activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / viral capsid / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 | |||||||||
Biological species | Human poliovirus 3 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Bahar, M.W. / Kotecha, A. / Fry, E.E. / Stuart, D.I. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Plant-made polio type 3 stabilized VLPs-a candidate synthetic polio vaccine. Authors: Johanna Marsian / Helen Fox / Mohammad W Bahar / Abhay Kotecha / Elizabeth E Fry / David I Stuart / Andrew J Macadam / David J Rowlands / George P Lomonossoff / Abstract: Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust ...Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material. In this study, we report the production of synthetically stabilized PV VLPs in plants. Mice carrying the gene for the human PV receptor are protected from wild-type PV when immunized with the plant-made PV sVLPs. Structural analysis of the stabilized mutant at 3.6 Å resolution by cryo-electron microscopy and single-particle reconstruction reveals a structure almost indistinguishable from wild-type PV3.Despite the success of current vaccination against poliomyelitis, safe, cheap and effective vaccines remain sought for continuing eradication effort. Here the authors use plants to express stabilized virus-like particles of type 3 poliovirus that can induce a protective immune response in mice transgenic for the human poliovirus receptor. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5o5b.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o5b.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o5b_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5o5b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5o5b_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 5o5b_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/5o5b ftp://data.pdbj.org/pub/pdb/validation_reports/o5/5o5b | HTTPS FTP |
-Related structure data
Related structure data | 3747MC 3749C 5o5pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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-Components
#1: Protein | Mass: 33562.785 Da / Num. of mol.: 1 / Mutation: T105M, F132L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895 |
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#2: Protein | Mass: 30188.982 Da / Num. of mol.: 1 / Mutation: L18I, L215M, D241E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895 |
#3: Protein | Mass: 26315.100 Da / Num. of mol.: 1 / Mutation: H19Y, L85F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895 |
#4: Protein | Mass: 7452.113 Da / Num. of mol.: 1 / Mutation: T67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895, UniProt: P03302*PLUS |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human poliovirus 3 / Type: VIRUS Details: Poliovirus type 3 (Saukett strain) virus-like particle produced in plant expression system. Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 5.8 MDa / Experimental value: NO |
Source (natural) | Organism: Human poliovirus 3 |
Source (recombinant) | Organism: Nicotiana benthamiana (plant) / Plasmid: pEAQ-HT |
Details of virus | Empty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Human poliovirus 3 / Strain: Saukett |
Virus shell | Name: Capsid / Diameter: 327 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 7 / Details: PBS pH 7.0 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Virus-like particles for polio type 3 (strain Saukett) were purified by Nycodenz gradients and assessed for monodispersity by negative stain EM analysis. |
Specimen support | Grid material: COPPER / Grid type: C-flat CF-2/1-2C |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Blot for 4 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 133333 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2768 |
Image scans | Sampling size: 14 µm / Width: 4086 / Height: 4086 / Movie frames/image: 33 / Used frames/image: 2-33 |
-Processing
Software | Name: PHENIX / Version: 1.12rc0_2787: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: The selected images were drift corrected using MotionCorr. | ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF parameters were estimated using CTFFIND3 as part of RELION 1.3. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 37378 Details: Automated particle picking (ETHAN) was followed by manual cleaning (EMAN2). | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4046 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: phenix.real_space_refine was used to refine the atomic model in the cryo-em map. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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