+Open data
-Basic information
Entry | Database: PDB / ID: 2xi3 | ||||||
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Title | HCV-H77 NS5B Polymerase Complexed With GTP | ||||||
Components | RNA-directed RNA polymeraseRNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / NONSTRUCTURAL PROTEIN / REPLICATION / RDRP / DE NOVO PRIMING / HEPACIVIRUS | ||||||
Function / homology | Function and homology information positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / 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 / structural molecule activity / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 2xi3.cif.gz | 454.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xi3.ent.gz | 370.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xi3 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xi3 | HTTPS FTP |
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-Related structure data
Related structure data | 2xhuC 2xhvC 2xhwC 2xi2C 1quvS 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: (-0.9936, -0.1133, 0.0021), Vector: |
-Components
#1: Protein | Mass: 63786.152 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 2421-2990 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate H77) / Strain: H77 / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27958, RNA-directed RNA polymerase #2: Chemical | ChemComp-GTP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.32 Å3/Da / Density % sol: 46.92 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: MES 50MM PH 6.5, AMMONIUM SULFATE 0.2M, AMMONIUM ACETATE 0.25M, PEG 1000 25%-30% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0448 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0448 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 121329 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUV Resolution: 1.7→34.654 Å / SU ML: 0.22 / σ(F): 1.96 / Phase error: 19.46 / 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: 45.563 Å2 / ksol: 0.413 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.654 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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