+Open data
-Basic information
Entry | Database: PDB / ID: 1ra7 | ||||||
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Title | Poliovirus Polymerase with GTP | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE / NUCLEOTIDYLTRANSFERASE / POLIOVIRUS / 3D / RNA-DEPENDENT / POLYMERASE / N-TERMINUS / GTP | ||||||
Function / homology | Function and homology information 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 ...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 / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Thompson, A.A. / Peersen, O.B. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. Authors: Thompson, A.A. / Peersen, O.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ra7.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ra7.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 1ra7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ra7_validation.pdf.gz | 774.5 KB | Display | wwPDB validaton report |
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Full document | 1ra7_full_validation.pdf.gz | 783.8 KB | Display | |
Data in XML | 1ra7_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 1ra7_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/1ra7 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/1ra7 | HTTPS FTP |
-Related structure data
Related structure data | 1ra6SC 1rajC 1tqlC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52987.859 Da / Num. of mol.: 1 / Fragment: RNA-directed RNA polymerase (residue 1748-2208) / Mutation: L446D, R455D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / Gene: 3D / Plasmid: pKKT7E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P03300, RNA-directed RNA polymerase | ||
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#2: Chemical | ChemComp-GTP / | ||
#3: Chemical | ChemComp-ACY / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.04 Å3/Da / Density % sol: 75.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium acetate, cacodylate, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 2003 |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. all: 43388 / Num. obs: 43388 / % possible obs: 98.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.13 / Num. unique all: 4210 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RA6 Resolution: 2.35→30 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: residues 132-135 have poor sidechain density and the model reflects the backbone path in this region of the structure
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Displacement parameters | Biso mean: 45.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.43 Å
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