+Open data
-Basic information
Entry | Database: PDB / ID: 2xi2 | |||||||||
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Title | HCV-H77 NS5B Apo Polymerase | |||||||||
Components | RNA-directed RNA polymerase | |||||||||
Keywords | TRANSFERASE / NONSTRUCTURAL PROTEIN / REPLICATION / RDRP / DE NOVO PRIMING | |||||||||
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 / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / 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 genotype 1a | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 2xi2.cif.gz | 662.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xi2.ent.gz | 549.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xi2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xi2_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 2xi2_full_validation.pdf.gz | 478.7 KB | Display | |
Data in XML | 2xi2_validation.xml.gz | 69.1 KB | Display | |
Data in CIF | 2xi2_validation.cif.gz | 101.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xi2 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xi2 | HTTPS FTP |
-Related structure data
Related structure data | 2xhuC 2xhvC 2xhwC 2xi3C 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.999, -0.0436, 0.0096), Vector: |
-Components
#1: Protein | Mass: 63786.152 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN, RESIDUES 2421-2990 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus genotype 1a (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-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLN2485 TO HIS ENGINEERED RESIDUE IN CHAIN B, GLN2485 TO HIS ...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: 2.27 Å3/Da / Density % sol: 45.75 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: MES 0.1M PH 6.5, AMMONIUM SULFATE 0.2M, PEG 5000 MONOMETHYL ETHER |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.07158 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07158 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.1 Å / Num. obs: 144615 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 16.56 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.9 / % possible all: 81.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUV Resolution: 1.8→43.053 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 20.25 / 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: 42.189 Å2 / ksol: 0.395 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.053 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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