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Yorodumi- PDB-5f3z: Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f3z | ||||||
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Title | Dengue serotype 3 RNA-dependent RNA polymerase bound to PC-79-SH52 | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE / RdRp Inhibitor / Dengue | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / 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 / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Noble, C.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening Authors: Noble, C.G. / Lim, S.P. / Arora, R. / Yokokawa, F. / Nilar, S. / Seh, C.C. / Wright, S.K. / Benson, T.E. / Smith, P.W. / Shi, P.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f3z.cif.gz | 147.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f3z.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f3z_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
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Full document | 5f3z_full_validation.pdf.gz | 456.3 KB | Display | |
Data in XML | 5f3z_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 5f3z_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f3z ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f3z | HTTPS FTP |
-Related structure data
Related structure data | 5f3tC 5f41C 4hhjS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 73624.867 Da / Num. of mol.: 1 / Fragment: UNP residues 2762-3390 / Mutation: G374E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6DLV0, UniProt: Q6YMS4*PLUS | ||||||
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#2: Chemical | #3: Chemical | ChemComp-5V5 / | #4: Water | ChemComp-HOH / | Sequence details | RESIDUE 374 GLU IS A NATURALLY OCCURRED MUTATION IN THE VIRAL SEQUENCE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M TRIS PH 8.0, 25% PEG 550 MME / PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→118.982 Å / Num. all: 55382 / Num. obs: 55382 / % possible obs: 98.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.62 Å2 / Rpim(I) all: 0.043 / Rrim(I) all: 0.105 / Rsym value: 0.095 / Net I/av σ(I): 6.667 / Net I/σ(I): 10.7 / Num. measured all: 291699 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HHJ Resolution: 2→29.28 Å / Cor.coef. Fo:Fc: 0.9304 / Cor.coef. Fo:Fc free: 0.9086 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.15 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.135
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Displacement parameters | Biso max: 167.18 Å2 / Biso mean: 41.13 Å2 / Biso min: 14.03 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→29.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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