|Entry||Database: EMDB / ID: EMD-5123|
|Title||RNA-releasing poliovirus intermediates|
|Keywords||Picornavirus / poliovirus / intermediate / RNA release / 80S|
|Function / homology|
Function and homology information
caveolin-mediated endocytosis of virus by host cell / suppression by virus of host MDA-5 activity / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / suppression by virus of host MAVS activity ...caveolin-mediated endocytosis of virus by host cell / suppression by virus of host MDA-5 activity / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / protein complex oligomerization / induction by virus of host autophagy / RNA-directed RNA polymerase / ion channel activity / suppression by virus of host gene expression / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / DNA replication / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3, picornavirus core protein 2A / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like ...Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3, picornavirus core protein 2A / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Peptidase C3A/C3B, picornaviral
Genome polyprotein / Genome polyprotein / Genome polyprotein
|Biological species||poliovirus 1 mahoney (poliovirus 1 mahoney)|
|Method||single particle reconstruction / cryo EM / negative staining / Resolution: 10 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.
|Validation Report||PDB-ID: 3iyb|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_5123.map.gz / Format: CCP4 / Size: 30.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.3223 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire 80S poliovirus
|Entire||Name: 80S poliovirus / Details: native virus heat-treated at 56 degrees C / Number of components: 1 / Oligomeric State: 60 promoters arranged as a icosahedron|
|Mass||Theoretical: 8.3 MDa / Experimental: 8.3 MDa / Measured by: Sedimentation|
-Component #1: virus, poliovirus 1 mahoney
|Virus||Name: poliovirus 1 mahoney / a.k.a: poliovirus 1 mahoney / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SEROTYPE|
|Mass||Theoretical: 8.3 MDa / Experimental: 8.3 MDa|
|Species||Species: poliovirus 1 mahoney (poliovirus 1 mahoney)|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Shell #1||Name of element: VP1 VP2 and VP3 / Diameter: 290 Å / T number (triangulation number): 1|
|Specimen||Specimen state: Particle / Method: negative staining, cryo EM|
|Sample solution||Specimen conc.: 0.2 mg/mL / Buffer solution: 20mM Tris, 50mM NaCl, 2 mM CaCl2 / pH: 7.4|
|Support film||200 mesh copper grids|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blot for 3 secs / Details: Vitrification instrument: home made plunger|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: OTHER|
|Lens||Magnification: 59000 X (nominal) / Imaging mode: OTHER / Defocus: 900 - 3000 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 138 / Scanner: ZEISS SCAI / Sampling size: 7 µm|
|Processing||Method: single particle reconstruction|
Details: 10,000 particle were partitioned into two distinct classes
Applied symmetry: I (icosahedral)
|3D reconstruction||Algorithm: PFT / Software: PFT2, EM3DR2 / CTF correction: each micrograph / Resolution: 10 Å / Resolution method: FSC 0.5|
-Atomic model buiding
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