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Yorodumi- PDB-5z3q: Crystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z3q | ||||||
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Title | Crystal Structure of a Soluble Fragment of Poliovirus 2C ATPase (2.55 Angstrom) | ||||||
Components | PV-2C | ||||||
Keywords | VIRAL PROTEIN / ATPase | ||||||
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 / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å | ||||||
Authors | Guan, H. / Tian, J. / Zhang, C. / Qin, B. / Cui, S. | ||||||
Funding support | China, 1items
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Citation | Journal: PLoS Pathog. / Year: 2018 Title: Crystal structure of a soluble fragment of poliovirus 2CATPase Authors: Guan, H. / Tian, J. / Zhang, C. / Qin, B. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z3q.cif.gz | 401.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z3q.ent.gz | 332.9 KB | Display | PDB format |
PDBx/mmJSON format | 5z3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/5z3q ftp://data.pdbj.org/pub/pdb/validation_reports/z3/5z3q | HTTPS FTP |
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-Related structure data
Related structure data | 5gq1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 23655.119 Da / Num. of mol.: 6 / Fragment: UNP residues 1243-1456 / Mutation: E207A, K209A,R149A Source method: isolated from a genetically manipulated source Details: synthetic / Source: (gene. exp.) Human poliovirus 1 Mahoney / Strain: Mahoney / Plasmid: pET 28a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: P03300, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.69 Å3/Da / Density % sol: 54.21 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MgCl2 0.2M, MES 0.1M pH 6.5, 3%(v/v) PGE4000, Polypropylene glycol P 400 (9.2% v/v) , 0.5mM TECP HCl PH range: 6.2-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2017 |
Radiation | Monochromator: Double Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 2.545→43.809 Å / Num. obs: 95988 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.42 % / CC1/2: 0.993 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.132 / Net I/av σ(I): 7.38 / Net I/σ(I): 7.56 |
Reflection shell | Resolution: 2.545→2.574 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 15058 / CC1/2: 0.468 / Rrim(I) all: 1.029 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GQ1 Resolution: 2.545→40.618 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.545→40.618 Å
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Refine LS restraints |
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LS refinement shell |
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