+Open data
-Basic information
Entry | Database: PDB / ID: 3iyc | |||||||||
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Title | Poliovirus late RNA-release intermediate | |||||||||
Components |
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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 | |||||||||
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 / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity ...: / 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 / 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 | Human poliovirus 1 Mahoney Poliovirus type 3 Poliovirus 1 Human poliovirus 1 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | |||||||||
Authors | Levy, H.C. / Bostina, M. / Filman, D.J. / Hogle, J.M. | |||||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3iyc.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iyc.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iyc_validation.pdf.gz | 749 KB | Display | wwPDB validaton report |
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Full document | 3iyc_full_validation.pdf.gz | 748.6 KB | Display | |
Data in XML | 3iyc_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 3iyc_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/3iyc ftp://data.pdbj.org/pub/pdb/validation_reports/iy/3iyc | HTTPS FTP |
-Related structure data
Related structure data | 5122MC 5123C 3iybC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 26558.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 1 Mahoney / References: UniProt: P03300 |
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#2: Protein/peptide | Mass: 1518.665 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) References: UniProt: P03302 |
#3: Protein | Mass: 25777.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Poliovirus 1 References: UniProt: Q9E8Z2, UniProt: Q9E912*PLUS, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: Protein | Mass: 27181.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 1 Mahoney / References: UniProt: P03300 |
#5: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 1 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 80S poliovirus / Type: VIRUS Details: 60 promoters arranged as a icosahedron. native virus heat-treated at 56 degrees C Synonym: poliovirus 1 mahoney |
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Molecular weight | Value: 8.3 MDa / Experimental value: YES |
Details of virus | Empty: YES / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | Name: 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl / pH: 7.4 / Details: 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20mM Tris, 50mM NaCl, 2 mM CaCl2 |
Specimen support | Details: quantifoil holey grids 1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blot for 3 secs |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 59000 X / Nominal defocus max: 3 nm / Nominal defocus min: 0.9 nm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: each micrograph | ||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||
3D reconstruction | Method: PFT / Resolution: 10 Å / Resolution method: FSC 0.5 CUT-OFF Details: ( Details about the particle: 10,000 particle were partitioned into two distinct classes ) Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--Rigid Body | ||||||||||||||||||||
Atomic model building | PDB-ID: 1POV Accession code: 1POV / Source name: PDB / Type: experimental model | ||||||||||||||||||||
Refinement step | Cycle: LAST
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