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Yorodumi- PDB-2who: CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS5B POLYMERASE FROM 1B GE... -
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-Basic information
Entry | Database: PDB / ID: 2who | |||||||||
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Title | CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS5B POLYMERASE FROM 1B GENOTYPE IN COMPLEX WITH A NON-NUCLEOSIDE INHIBITOR | |||||||||
Components | RNA-DIRECTED RNA POLYMERASE | |||||||||
Keywords | TRANSFERASE / RNA REPLICATION / ENVELOPE PROTEIN / HEPATITIS C VIRUS / ENDOPLASMIC RETICULUM / NON NUCLEOSIDE INHIBITOR / VIRAL PROTEIN / METAL-BINDING / TRANSMEMBRANE / POLYMERASE / ATP-BINDING / GENOTYPE 1B / RNA-BINDING / RNA-DEPENDENT RNA POLYMERASE / NNI / HCV / NS5B / MEMBRANE / HELICASE / HYDROLASE / NUCLEOTIDE-BINDING / ALLOSTERIC INHIBITOR / RNA-DIRECTED RNA POLYMERASE | |||||||||
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 / 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 / virion attachment to host cell / apoptotic process / structural molecule activity / host cell plasma membrane / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Di Marco, S. | |||||||||
Citation | Journal: J. Med. Chem. / Year: 2009 Title: Identification and biological evaluation of a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as hepatitis C virus NS5B polymerase inhibitors. Authors: Ontoria, J.M. / Rydberg, E.H. / Di Marco, S. / Tomei, L. / Attenni, B. / Malancona, S. / Martin Hernando, J.I. / Gennari, N. / Koch, U. / Narjes, F. / Rowley, M. / Summa, V. / Carroll, S.S. ...Authors: Ontoria, J.M. / Rydberg, E.H. / Di Marco, S. / Tomei, L. / Attenni, B. / Malancona, S. / Martin Hernando, J.I. / Gennari, N. / Koch, U. / Narjes, F. / Rowley, M. / Summa, V. / Carroll, S.S. / Olsen, D.B. / De Francesco, R. / Altamura, S. / Migliaccio, G. / Carfi, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2who.cif.gz | 227.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2who.ent.gz | 182.3 KB | Display | PDB format |
PDBx/mmJSON format | 2who.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/2who ftp://data.pdbj.org/pub/pdb/validation_reports/wh/2who | HTTPS FTP |
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-Related structure data
Related structure data | 1csjS 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 oper: (Code: given Matrix: (-1, -0.00056, -0.00077), Vector: |
-Components
#1: Protein | Mass: 59641.508 Da / Num. of mol.: 2 / Fragment: NS5B, RESIDUES 2420-2955 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HEPATITIS C VIRUS / Strain: ISOLATE BK / Description: GENBANK ACCESSION NUMBER AB016785 / Variant: GENOTYPE 1B / Plasmid: PT7.7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26663, RNA-directed RNA polymerase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | NS5B PROTEIN, GENOTYPE 1B AND STRAIN BK, LACKING THE C- TERMINAL 55 AMINO ACIDS. TOTAL AMINO ACIDS ...NS5B PROTEIN, GENOTYPE 1B AND STRAIN BK, LACKING THE C- TERMINAL 55 AMINO ACIDS. TOTAL AMINO ACIDS 535, UNIPROT REFERENCE P26663, 2420-2955 | |
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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: 2.56 Å3/Da / Density % sol: 51.55 % / Description: NONE |
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Crystal grow | pH: 6 / Details: pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 60884 / % possible obs: 74.3 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.5 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CSJ Resolution: 2→95.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.023 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FINAL MODEL ENCOMPASS RESIDUES 1-531, RESIDUES 532-536 ARE NOT IN DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.734 Å2
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Refinement step | Cycle: LAST / Resolution: 2→95.35 Å
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