+Open data
-Basic information
Entry | Database: PDB / ID: 8ay5 | ||||||
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Title | Human rhinovirus 2 empty particle in situ | ||||||
Components |
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Keywords | VIRUS / Human rhinovirus 2 / empty particle / in situ / cryo-EM. | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / 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 | rhinovirus A2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å | ||||||
Authors | Ishemgulova, A. / Mukhamedova, L. / Trebichalska, Z. / Payne, P. / Smerdova, L. / Moravcova, J. / Hrebik, D. / Buchta, D. / Skubnik, K. / Fuzik, T. ...Ishemgulova, A. / Mukhamedova, L. / Trebichalska, Z. / Payne, P. / Smerdova, L. / Moravcova, J. / Hrebik, D. / Buchta, D. / Skubnik, K. / Fuzik, T. / Novacek, J. / Plevka, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: To Be Published Title: Endosome rupture enables enteroviruses to infect cells. Authors: Ishemgulova, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ay5.cif.gz | 250.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ay5.ent.gz | 204.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ay5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ay5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8ay5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8ay5_validation.xml.gz | 33 KB | Display | |
Data in CIF | 8ay5_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/8ay5 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/8ay5 | HTTPS FTP |
-Related structure data
Related structure data | 15711MC 8ay4C 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: 28851.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells. References: UniProt: P04936 |
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#2: Protein | Mass: 27899.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells. References: UniProt: P04936 |
#3: Protein | Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2 Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells. References: UniProt: P04936 |
-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: rhinovirus A2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: rhinovirus A2 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 332 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |