|Entry||Database: EMDB / ID: 5123|
|Title||RNA-releasing poliovirus intermediates|
|Map data||this is poliovirus in the early stage of RNA release|
|Keywords||Picornavirus / poliovirus / intermediate / RNA release / 80S|
|Function / homology||Viral coat protein subunit / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A ...Viral coat protein subunit / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like / Peptidase S1, PA clan / RdRp of positive ssRNA viruses catalytic domain profile. / Picornavirus core protein 2A / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / P-loop containing nucleoside triphosphate hydrolase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Picornavirus 2B protein / RNA helicase / RNA dependent RNA polymerase / caveolin-mediated endocytosis of virus by host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / T=pseudo3 icosahedral viral capsid / 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 / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / suppression by virus of host gene expression / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / DNA replication / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein|
Function and homology information
|Source||poliovirus 1 mahoney (poliovirus 1 mahoney)|
|Method||single particle reconstruction / cryo EM / negative staining / 10 Å resolution|
|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
|Validation Report||PDB-ID: 3iyb|
SummaryFull reportAbout validation report
|Date||Deposition: Jul 16, 2009 / Header (metadata) release: Jul 31, 2009 / Map release: Mar 10, 2010 / Last update: Sep 23, 2011|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5123.map.gz (map file in CCP4 format, 31723 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.3223 Å|
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 microns|
|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
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi