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Yorodumi- PDB-2im3: Crystal structure of poliovirus polymerase complexed with UTP and Mn2+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 2im3 | ||||||
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Title | Crystal structure of poliovirus polymerase complexed with UTP and Mn2+ | ||||||
Components | poliovirus polymerase | ||||||
Keywords | TRANSFERASE / nucleotidyltransferase / poliovirus / 3d / rna-dependent / polymerase / UTP / stabilization | ||||||
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 MDA-5 activity / 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 MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / 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 MDA-5 activity / 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 MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Human poliovirus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Thompson, A.A. / Peersen, O.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Stabilization of Poliovirus Polymerase by NTP Binding and Fingers-Thumb Interactions. Authors: Thompson, A.A. / Albertini, R.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 | 2im3.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2im3.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 2im3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/2im3 ftp://data.pdbj.org/pub/pdb/validation_reports/im/2im3 | HTTPS FTP |
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-Related structure data
Related structure data | 2ilyC 2ilzC 2im0C 2im1C 2im2C 1ra6S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52987.859 Da / Num. of mol.: 1 / Fragment: RNA-directed RNA polymerase, residues 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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-Non-polymers , 5 types, 115 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-UTP / | #5: Chemical | ChemComp-ACY / #6: Water | ChemComp-HOH / | |
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-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 |
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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 / Detector: IMAGE PLATE |
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: 2.6→30 Å / Num. all: 32149 / Num. obs: 32149 / % possible obs: 99.3 % / Redundancy: 8.61 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.09 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 8.54 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 3217 / Rsym value: 0.458 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RA6 Resolution: 2.6→29.7 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: THE STRUCTURE WAS REFINED WITH ANOMALOUS DATA TO ACCOUNT FOR SIGNIFICANT ANOMALOUS SIGNAL FROM ARSENIC, WHICH IS FOUND IN SEVERAL CAS RESIDUES IN THE STRUCTURE. HOWEVER, THE DATA REDUCTION ...Details: THE STRUCTURE WAS REFINED WITH ANOMALOUS DATA TO ACCOUNT FOR SIGNIFICANT ANOMALOUS SIGNAL FROM ARSENIC, WHICH IS FOUND IN SEVERAL CAS RESIDUES IN THE STRUCTURE. HOWEVER, THE DATA REDUCTION AND COMPLETENESS STATISTICS ARE BASED ON MERGING ANOMALOUS REFLECTIONS. 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: 49 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.7 Å
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Refine LS restraints |
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