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Yorodumi- PDB-2hfz: Crystal structure of RNA dependent RNA polymerase domain from Wes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hfz | ||||||
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Title | Crystal structure of RNA dependent RNA polymerase domain from West Nile virus | ||||||
Components | RNA-directed RNA polymerase(NS5) | ||||||
Keywords | TRANSFERASE / West Nile Virus RNA polymerase / Structural Genomics / Marseilles Structural Genomics Program @ AFMB / MSGP / VIZIER / Viral enzymes involved in replication | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / 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 / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Kunjin virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Egloff, M.P. / Malet, H. / Marseilles Structural Genomics Program @ AFMB (MSGP) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of the RNA polymerase domain of the West Nile virus non-structural protein 5 Authors: Malet, H. / Egloff, M.P. / Selisko, B. / Butcher, R.E. / Wright, P.J. / Roberts, M. / Gruez, A. / Sulzenbacher, G. / Vonrhein, C. / Bricogne, G. / Mackenzie, J.M. / Khromykh, A.A. / Davidson, A.D. / Canard, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hfz.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hfz.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/2hfz ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hfz | HTTPS FTP |
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-Related structure data
Related structure data | 2hcnC 2hcsSC 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
#1: Protein | Mass: 73758.562 Da / Num. of mol.: 1 / Fragment: RNA-directed RNA polymerase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kunjin virus / Genus: Flavivirus / Species: West Nile virus / Strain: kunjin / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): C41pRos / References: UniProt: P14335, RNA-directed RNA polymerase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Sequence details | Sequence Lys 273 has been cloned on purpose for expression improvement |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: 5-25% PEG 1000 0.1 M NaCacodylate 0.3 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3→21.77 Å / Num. obs: 14328 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 70.71 Å2 / Rsym value: 0.097 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.337 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HCS Resolution: 3→95.35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso mean: 89.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.63 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→95.35 Å
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LS refinement shell | Resolution: 3→3.18 Å / Total num. of bins used: 9
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