+Open data
-Basic information
Entry | Database: PDB / ID: 1c2p | ||||||
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Title | HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE | ||||||
Components | RNA-DEPENDENT RNA POLYMERASE | ||||||
Keywords | TRANSFERASE / POLYMERASE RNA-DEPENDENT RNA POLYMERASE HEPATITIS C VIRUS NS5B APOENZYME | ||||||
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 / 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 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Lesburg, C.A. / Cable, M.B. / Ferrari, E. / Hong, Z. / Mannarino, A.F. / Weber, P.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Authors: Lesburg, C.A. / Cable, M.B. / Ferrari, E. / Hong, Z. / Mannarino, A.F. / Weber, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c2p.cif.gz | 236.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c2p.ent.gz | 197.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c2p_validation.pdf.gz | 380 KB | Display | wwPDB validaton report |
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Full document | 1c2p_full_validation.pdf.gz | 391.4 KB | Display | |
Data in XML | 1c2p_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 1c2p_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/1c2p ftp://data.pdbj.org/pub/pdb/validation_reports/c2/1c2p | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64529.168 Da / Num. of mol.: 2 / Fragment: HCV NS5B Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P26663, RNA-directed RNA polymerase #2: 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: 2.25 Å3/Da / Density % sol: 45.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: batch / pH: 5 Details: PEG 4000, GLYCEROL, DTT, MES, NACL, pH 5, BATCH, temperature 22K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 85549 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.252 / % possible all: 82 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Num. measured all: 404133 |
Reflection shell | *PLUS % possible obs: 82 % / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Resolution: 1.9→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |