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Yorodumi- PDB-4aex: HCV-JFH1 NS5B POLYMERASE STRUCTURE AT 2.4 ANGSTROM in a primitive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aex | ||||||
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Title | HCV-JFH1 NS5B POLYMERASE STRUCTURE AT 2.4 ANGSTROM in a primitive orthorhombic space group | ||||||
Components | RNA-DIRECTED RNA POLYMERASERNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / HEPACIVIRUS / NONSTRUCTURAL PROTEINS / REPLICATION / DE NOVO INITIATION / PRIMING | ||||||
Function / homology | Function and homology information negative regulation of autophagy of mitochondrion / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity ...negative regulation of autophagy of mitochondrion / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / negative regulation of autophagy / SH3 domain binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | HEPATITIS C VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Caillet-Saguy, C. / Bressanelli, S. | ||||||
Citation | Journal: J.Virol. / Year: 2012 Title: Two Crucial Early Steps in RNA Synthesis by the Hepatitis C Virus Polymerase Involve a Dual Role of Residue 405. Authors: Scrima, N. / Caillet-Saguy, C. / Ventura, M. / Harrus, D. / Astier-Gin, T. / Bressanelli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aex.cif.gz | 444.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aex.ent.gz | 367.6 KB | Display | PDB format |
PDBx/mmJSON format | 4aex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/4aex ftp://data.pdbj.org/pub/pdb/validation_reports/ae/4aex | HTTPS FTP |
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-Related structure data
Related structure data | 4adpC 4aepC 2xxdS C: citing same article (ref.) 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.9976, 0.0678, -0.0162), Vector: |
-Components
#1: Protein | Mass: 64631.152 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 2442-3013 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HEPATITIS C VIRUS / Strain: JFH1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q99IB8, RNA-directed RNA polymerase #2: Chemical | ChemComp-PO4 / | #3: 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: 2.59 Å3/Da / Density % sol: 52.42 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.2 M SODIUM PHOSPHATE PH 6.5, 8-12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→40.75 Å / Num. obs: 51101 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 28.55 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.41→2.48 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XXD Resolution: 2.41→40.746 Å / SU ML: 0.68 / σ(F): 2 / Phase error: 21.78 / Stereochemistry target values: ML Details: SOFT TORSION NCS RESTRAINTS WERE ENFORCED IN REFINEMENT BETWEEN THE TWO MOLECULES IN THE ASYMMETRIC UNIT.
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.939 Å2 / ksol: 0.352 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→40.746 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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