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Yorodumi- PDB-8ayx: Poliovirus type 3 (strain Saukett) stabilised virus-like particle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ayx | ||||||
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Title | Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) in complex with GSH and GPP3 | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Capsid protein / Glutathione / inhibitor / complex | ||||||
Function / homology | Function and homology information symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | Human poliovirus 3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | Bahar, M.W. / Fry, E.E. / Stuart, D.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2022 Title: A conserved glutathione binding site in poliovirus is a target for antivirals and vaccine stabilisation. Authors: Mohammad W Bahar / Veronica Nasta / Helen Fox / Lee Sherry / Keith Grehan / Claudine Porta / Andrew J Macadam / Nicola J Stonehouse / David J Rowlands / Elizabeth E Fry / David I Stuart / Abstract: Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or ...Strategies to prevent the recurrence of poliovirus (PV) after eradication may utilise non-infectious, recombinant virus-like particle (VLP) vaccines. Despite clear advantages over inactivated or attenuated virus vaccines, instability of VLPs can compromise their immunogenicity. Glutathione (GSH), an important cellular reducing agent, is a crucial co-factor for the morphogenesis of enteroviruses, including PV. We report cryo-EM structures of GSH bound to PV serotype 3 VLPs showing that it can enhance particle stability. GSH binds the positively charged pocket at the interprotomer interface shown recently to bind GSH in enterovirus F3 and putative antiviral benzene sulphonamide compounds in other enteroviruses. We show, using high-resolution cryo-EM, the binding of a benzene sulphonamide compound with a PV serotype 2 VLP, consistent with antiviral activity through over-stabilizing the interprotomer pocket, preventing the capsid rearrangements necessary for viral infection. Collectively, these results suggest GSH or an analogous tight-binding antiviral offers the potential for stabilizing VLP vaccines. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ayx.cif.gz | 147.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ayx.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ayx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/8ayx ftp://data.pdbj.org/pub/pdb/validation_reports/ay/8ayx | HTTPS FTP |
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-Related structure data
Related structure data | 15725MC 8ayyC 8ayzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 33562.785 Da / Num. of mol.: 1 / Mutation: VP1 T105M, VP1 F132L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Cell line (production host): PichiaPink / Production host: Komagataella pastoris (fungus) / References: UniProt: Q84895 |
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#2: Protein | Mass: 37623.023 Da / Num. of mol.: 1 / Mutation: VP2 L18I, VP2 L215M, VP2 D241E, VP4 T67A Source method: isolated from a genetically manipulated source Details: Sequence is given for the VP0 polypeptide. Mutations are numbered according to sequence numbering for mature polypeptides VP2 and VP4. Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Cell line (production host): PichiaPink / Production host: Komagataella pastoris (fungus) / References: UniProt: Q84895 |
#3: Protein | Mass: 26315.100 Da / Num. of mol.: 1 / Mutation: VP3 H19Y, VP3 L85F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Cell line (production host): PichiaPink / Production host: Komagataella pastoris (fungus) / References: UniProt: Q84895 |
#4: Chemical | ChemComp-YM2 / |
#5: Chemical | ChemComp-GSH / |
Has ligand of interest | Y |
-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: Recombinantly expressed virus-like particle of poliovirus type 3 (strain Saukett). Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 5.85 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Human poliovirus 3 / Strain: Saukett | ||||||||||||
Source (recombinant) | Organism: Komagataella pastoris (fungus) / Cell: PichiaPink | ||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE | ||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||
Virus shell | Name: Virus shell 1 / Diameter: 310 nm / Triangulation number (T number): 1 | ||||||||||||
Buffer solution | pH: 7 / Details: 1 x DPBS, 20 mM EDTA, pH 7.0 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Virus-like particle purified by sucrose density gradient purification from Pichia pastoris cells. | ||||||||||||
Specimen support | Details: The specific type of grid used was Ultra-thin carbon support film, 3nm - on lacey carbon AGS187-4 from Agar Scientific. Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: 4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV. |
-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: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 69.78 sec. / Electron dose: 34.89 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2503 / Details: Pixel sampling of 1.08 A/pixel. |
Image scans | Sampling size: 14 µm |
-Processing
EM software |
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Image processing | Details: Pixels size was 1.08 A/pixel. All frames were used for motion correction. | ||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 19622 / Details: Automated particle picking using crYOLO. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5364 / Algorithm: BACK PROJECTION Details: Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -52.3 Angstroms. Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 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 building | PDB-ID: 1PVC Accession code: 1PVC / Source name: PDB / Type: experimental model |