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Open data
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Basic information
Entry | Database: PDB / ID: 8ay4 | ||||||
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Title | Human rhinovirus 2 virion in situ | ||||||
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![]() | VIRUS / Human rhinovirus 2 / in situ / cryo-EM. | ||||||
Function / homology | ![]() 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 / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
![]() | 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 | ![]()
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![]() | ![]() Title: Endosome rupture enables enteroviruses to infect cells. Authors: Ishemgulova, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263.1 KB | Display | ![]() |
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PDB format | ![]() | 215.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15710MC ![]() 8ay5C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 30645.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() 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) ![]() 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) ![]() 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 |
#4: Protein/peptide | Mass: 2810.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: rhinovirus A2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / 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 / Humidity: 100 % |
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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: ![]() |
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 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
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Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / 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: 1590 / Details: Particles were picked manually. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1424 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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