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RNA-releasing poliovirus intermediates
by single particle (icosahedral) reconstruction, at 10 A resolution
#1: Surface view with section colored by density value, Surface level: 20.501312207, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 20.501312207, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3iyc, Surface level: 20.501312207, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-3iyc, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5122 |
|---|---|
| Title | RNA-releasing poliovirus intermediates |
| Map | LATE early RNA-releasing 80S poliovirus |
| Sample | 80S poliovirus |
| Keywords |  Picornavirus, poliovirus, intermediate, RNA-release, 80S |
| Authors | Levy HC, Bostina M, Filman DJ, Hogle JM |
| Date | Deposition: 2009-06-15, Header release: 2009-07-31, Map release: 2010-03-10, Last update: 2011-09-27 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 20.501312207, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 20.501312207, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3iyc, Surface level: 20.501312207, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-3iyc, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Virol., Vol. 84, Issue 9, Page 4426-41, 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 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. |
| Keywords | Cryoelectron Microscopy, HeLa Cells, Humans, Imaging, Three-Dimensional, Models, Molecular, Poliovirus (physiology), Protein Structure, Quaternary, RNA, Viral (metabolism), Virion (ultrastructure), Virus Internalization |
| Links | DOI: 10.1128/JVI.02393-09, PubMed: 20181687, PMC: PMC2863768 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5122.map ( map file in CCP4 format, 32484 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 466.782 A , B = 466.782 A , C = 466.782 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.3223 A , Y = 2.3223 A , Z = 2.3223 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | LATE early RNA-releasing 80S poliovirus | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | 80S poliovirus |
|---|---|
| Number of Components | 1 |
| Oligomeric State | 60 promoters arranged as a icosahedron |
| Theoretical Mass | 8.3 MDa |
| Details | native virus heat-treated at 56 degrees C |
| Mass-estimation Method | Sedimentation |
| Experimental Mass | 8.3 MDa |
| Component #1: virus - poliovirus 1 mahoney | |
| Scientific name | poliovirus 1 mahoney |
| Theoretical Mass | 8.3 MDa |
| Experimental Mass | 8.3 MDa |
| Details | native virus is converted by heat-treatment to 80S |
| Scientific Name of Species | poliovirus 1 mahoney |
| Common Name of Species | poliovirus 1 mahoney |
| Empty | Yes |
| Enveloped | No |
| Isolate | SEROTYPE |
| Class | VIRION |
| Natural Source | Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: VERTEBRATES |
| Shell | Diameter: 290 A Name Element: capsid T Number: 1 |
 Experiment | |
| Sample Preparation | |
| Staining | not stained |
|---|---|
| Specimen Conc | 0.2 mg/ml |
| Specimen Support Details | 200 mesh copper grids |
| Specimen State | particle |
| Buffer | Details: 20mM Tris, 50mM NaCl, 2 mM CaCl2 pH: 7.4 |
| Vitrification | |
| Method | blot for 3 secs |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: home made plunger |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI TECNAI F30 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 15 e/A**2 |
| Illumination Mode | OTHER |
| Lens | |
| Magnification | Nominal: 59000 X, |
| Imaging Mode | OTHER |
| Defocus | 900 nm - 3000 nm |
| Specimen Holder | |
| Holder | Eucentric ( GATAN LIQUID NITROGEN ) |
| Camera | |
| Detector | Kodak SO163 |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 138 |
| Sampling Size | 7 microns |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | PFT |
| Software | PFT2, EM3DR2 |
| CTF Correction | each micrograph |
| Resolution By Author | 10 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | 10,000 particle were partitioned into two distinct classes |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid Body |
| Software | INSOUT |
| Refinement Protocol | rigid body |
| Refinement Space | RECIPROCAL |
| Fitted Coordinate | |
| PDB entry ID | |
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