+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5123 | |||||||||
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Title | RNA-releasing poliovirus intermediates | |||||||||
Map data | this is poliovirus in the early stage of RNA release | |||||||||
Sample |
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Keywords | Picornavirus / poliovirus / intermediate / RNA release / 80S | |||||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / 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 / 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 ...caveolin-mediated endocytosis of virus by host cell / 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 / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / symbiont-mediated suppression of host innate immune response / 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 | poliovirus 1 mahoney | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 10.0 Å | |||||||||
Authors | Levy HC / Bostina M / Filman DJ / Hogle JM | |||||||||
Citation | Journal: J Virol / Year: 2010 Title: Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. Authors: Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle / Abstract: Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes ...Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes associated with the release of the RNA genome, we have used cryo-electron microscopy to characterize the structure of the 80S "empty" particles of poliovirus that are thought to represent the final product of the cell entry pathway. Using two-dimensional classification methods, we show that preparations of 80S particles contain at least two structures, which might represent snapshots from a continuous series of conformers. Using three-dimensional reconstruction methods, we have solved the structure of two distinct forms at subnanometric resolution, and we have built and refined pseudoatomic models into the reconstructions. The reconstructions and the derived models demonstrate that the two structural forms are both slightly expanded, resulting in partial disruption of interprotomer interfaces near their particle 2-fold axes, which may represent the site where RNA is released. The models demonstrate that each of the two 80S structures has undergone a unique set of movements of the capsid proteins, associated with rearrangement of flexible loops and amino-terminal extensions that participate in contacts between protomers, between pentamers, and with the viral RNA. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5123.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-5123-v30.xml emd-5123.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_5123_1.tif | 1.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5123 | HTTPS FTP |
-Validation report
Summary document | emd_5123_validation.pdf.gz | 336.2 KB | Display | EMDB validaton report |
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Full document | emd_5123_full_validation.pdf.gz | 335.8 KB | Display | |
Data in XML | emd_5123_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5123 | HTTPS FTP |
-Related structure data
Related structure data | 3iybMC 5122C 3iycC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5123.map.gz / Format: CCP4 / Size: 30.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | this is poliovirus in the early stage of RNA release | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.3223 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 80S poliovirus
Entire | Name: 80S poliovirus |
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Components |
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-Supramolecule #1000: 80S poliovirus
Supramolecule | Name: 80S poliovirus / type: sample / ID: 1000 / Details: native virus heat-treated at 56 degrees C / Oligomeric state: 60 promoters arranged as a icosahedron / Number unique components: 1 |
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Molecular weight | Experimental: 8.3 MDa / Theoretical: 8.3 MDa / Method: Sedimentation |
-Supramolecule #1: poliovirus 1 mahoney
Supramolecule | Name: poliovirus 1 mahoney / type: virus / ID: 1 / Name.synonym: poliovirus 1 mahoney / Sci species name: poliovirus 1 mahoney / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: poliovirus 1 mahoney |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Experimental: 8.3 MDa / Theoretical: 8.3 MDa |
Virus shell | Shell ID: 1 / Name: VP1 VP2 and VP3 / Diameter: 290 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 / Details: 20mM Tris, 50mM NaCl, 2 mM CaCl2 |
Staining | Type: NEGATIVE / Details: not stained |
Grid | Details: 200 mesh copper grids |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home made plunger / Method: blot for 3 secs |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 138 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | 10,000 particle were partitioned into two distinct classes |
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CTF correction | Details: each micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT2, EM3DR2 |