+Open data
-Basic information
Entry | Database: PDB / ID: 2xhu | |||||||||
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Title | HCV-J4 NS5B Polymerase Orthorhombic Crystal Form | |||||||||
Components | RNA-directed RNA polymerase | |||||||||
Keywords | TRANSFERASE / REPLICATION / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / 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 / molecular adaptor activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Hepatitis C virus genotype 1b | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.287 Å | |||||||||
Authors | Harrus, D. / Ahmed-El-Sayed, N. / Simister, P.C. / Miller, S. / Triconnet, M. / Hagedorn, C.H. / Mahias, K. / Rey, F.A. / Astier-Gin, T. / Bressanelli, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Further Insights Into the Roles of GTP and the C- Terminus of the Hepatitis C Virus Polymerase in the Initiation of RNA Synthesis Authors: Harrus, D. / Ahmed-El-Sayed, N. / Simister, P.C. / Miller, S. / Triconnet, M. / Hagedorn, C.H. / Mahias, K. / Rey, F.A. / 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 | 2xhu.cif.gz | 460.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xhu.ent.gz | 380.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xhu_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 2xhu_full_validation.pdf.gz | 469.2 KB | Display | |
Data in XML | 2xhu_validation.xml.gz | 48 KB | Display | |
Data in CIF | 2xhu_validation.cif.gz | 69.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/2xhu ftp://data.pdbj.org/pub/pdb/validation_reports/xh/2xhu | HTTPS FTP |
-Related structure data
Related structure data | 2xhvC 2xhwC 2xi2C 2xi3C 1nb4S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 64598.988 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 2420-2989 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus genotype 1b (strain HC-J4) Strain: J4 / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O92972, RNA-directed RNA polymerase #2: Chemical | ChemComp-SO4 / #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: 2.98 Å3/Da / Density % sol: 58.73 % / Description: NONE |
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Crystal grow | pH: 7 / Details: MAGNESIUM SULFATE 0.2M, PEG 2000 MME 15%-25%, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.1 Å / Num. obs: 69005 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 25.59 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.36 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NB4 Resolution: 2.287→48.101 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 20.43 / Stereochemistry target values: ML / Details: RESIDUES 563-569 ARE DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.611 Å2 / ksol: 0.357 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.287→48.101 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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