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Poliovirus early RNA-release intermediate
by single particle (icosahedral) reconstruction, at 10 A resolution
#1: Biological unit as complete icosahedral assembly, Made by Jmol
#2: Biological unit as icosahedral pentamer, Made by Jmol
#3: Biological unit as icosahedral 23 hexamer, Made by Jmol
#4: Depositted structure unit, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-5123, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-5123, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3iyb |
|---|---|
| Title | Poliovirus early RNA-release intermediate |
| Descriptor | Genome polyprotein (E.C.3.4.22.29 3.6.1.15 3.4.22.28 2.7.7.48) Precursor polyprotein VP1 core |
| Keywords |  VIRAL PROTEIN, Picornavirus, poliovirus, intermediate, RNA release, 80S, ATP-binding, Capsid protein, Covalent protein-RNA linkage, Cytoplasmic vesicle, Helicase, Host-virus interaction, Hydrolase, Lipoprotein, Membrane, Myristate, Nucleotide-binding, Nucleotidyltransferase, Phosphoprotein, Protease, RNA replication, RNA-binding, RNA-directed RNA polymerase, Thiol protease, Transferase, Virion |
| Authors | Levy, H.C., Bostina, M., Filman, D.J., Hogle, J.M. |
| Date | Deposition: 2009-07-21, Release: 2010-03-16 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie Page#1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-5123, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5123, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map 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 |
 Components | |
| ID 1 : Protein VP0, VP4-VP2, Protein VP4, Virion protein 4, P1A, Protein VP2, Virion protein 2, P1B, Protein VP3, Virion protein 3, P1C, Protein VP1, Virion protein 1, P1D, Picornain 2A, Protein 2A, P2A, Protein 2B, P2B, Protein 2C, P2C, Protein 3A, P3A, Protein 3B, P3B, VPg, Picornain 3C, Protease 3C, P3C, RNA-directed RNA polymerase 3D-POL, P3D-POL | |
| Image |   |
|---|---|
| Description | Genome polyprotein |
| Type | polymer |
| Formula weight | 26559.176 Da |
| Number of molecules | 1 |
| Ec | 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:12081, Human poliovirus 1 Mahoney |
| Links | UniProt: P03300, Sequence view |
| ID 2 : Protein VP0, VP4-VP2, Protein VP4, Virion protein 4, P1A, Protein VP2, Virion protein 2, P1B, Protein VP3, Virion protein 3, P1C, Protein VP1, Virion protein 1, P1D, Picornain 2A, Protein 2A, P2A, Protein 2B, P2B, Protein 2C, P2C, Protein 3A, P3A, Protein 3B, P3B, VPg, Picornain 3C, Protease 3C, P3C, RNA-directed RNA polymerase 3D-POL, P3D-POL | |
| Image |   |
| Description | Genome polyprotein |
| Type | polymer |
| Formula weight | 1518.680 Da |
| Number of molecules | 1 |
| Ec | 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:12088, Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) |
| Links | UniProt: P03302, Sequence view |
| ID 3 : Precursor polyprotein | |
| Image |   |
| Description | Precursor polyprotein |
| Type | polymer |
| Formula weight | 25777.738 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:12080, Human poliovirus 1 |
| Links | UniProt: Q9E912, Sequence view |
| ID 4 : Protein VP0, VP4-VP2, Protein VP4, Virion protein 4, P1A, Protein VP2, Virion protein 2, P1B, Protein VP3, Virion protein 3, P1C, Protein VP1, Virion protein 1, P1D, Picornain 2A, Protein 2A, P2A, Protein 2B, P2B, Protein 2C, P2C, Protein 3A, P3A, Protein 3B, P3B, VPg, Picornain 3C, Protease 3C, P3C, RNA-directed RNA polymerase 3D-POL, P3D-POL | |
| Image |   |
| Description | Genome polyprotein |
| Type | polymer |
| Formula weight | 27181.799 Da |
| Number of molecules | 1 |
| Ec | 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:12081, Human poliovirus 1 Mahoney |
| Links | UniProt: P03300, Sequence view |
| ID 5 : VP1 core | |
| Image |   |
| Description | VP1 core |
| Type | polymer |
| Formula weight | 954.175 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:12080, Human poliovirus 1 |
| Links | Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Composition | 60 promoters arranged as a icosahedron |
| Details | native virus heat-treated at 56 degrees C |
| Experimental Mass | 8.3 |
| Mass-estimation Method | Sedimentation |
| Theoretical Mass | 8.3 |
| Name | 80S poliovirus |
| Num components | 1 |
| Entity assembly | |
| Name | poliovirus 1 mahoney |
| Type | VIRUS |
| Virus entity | |
| Empty | YES |
| Enveloped | NO |
| Ictvdb id | 00.052.0.01.001 |
| Virus host category | VERTEBRATES |
| Virus host species | Homo sapiens |
| Virus isolate | SEROTYPE |
| Virus type | VIRION |
| Buffer | |
| Name | 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| Details | 20mM Tris, 50mM NaCl, 2 mM CaCl2 |
| Entity assembly id | 1 |
| pH | 7.4 |
| Sample concentration | 0.2 mg/ml |
| Vitrification | |
| Cryogen name | ETHANE |
| Instrument | home made plunger |
| Method | blot for 3 secs |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI TECNAI F30 |
|---|---|
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Electron dose | 15 e/A**2 |
| Illumination mode | OTHER |
| Lens | |
| Mode | OTHER |
| Magnification | nominal: 59000 X |
| Detector distance | 0.0 |
| Nominal defocus | max: 3.0 nm, min: 0.9 nm |
| Specimen holder | |
| Specimen holder | model: GATAN LIQUID NITROGEN, type: Eucentric |
| Tilt angle | min: 0.0 degrees, max: 0.0 degrees |
| Detector | |
| Type | Kodak SO163 |
 Processing | |
| 2D projection selection | |
| Software name | INSOUT |
|---|---|
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| CTF correction method | each micrograph |
| Details | Details about the particle: 10,000 particle were partitioned into two distinct classes |
| Method | PFT |
| Resolution | 10 A |
| Resolution method | FSC at 0.5 cut-off |
| Software | PFT2, EM3DR2 |
| 3D fitting | |
| Refinement Protocol | Rigid Body |
| Refinement Space | RECIPROCAL |
| Software name | INSOUT |
| Refine hist | |
| Total atoms | 723 |
| Protein atoms | 723 |
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