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Yorodumi- PDB-1r6a: Structure of the dengue virus 2'O methyltransferase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r6a | ||||||
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Title | Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate | ||||||
Components | Genome polyprotein | ||||||
Keywords | TRANSFERASE / ribavirin 5'-triphosphate / dengue virus / 2'O methyltransferase | ||||||
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 / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...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 / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / 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 / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 Puerto Rico/PR159-S1/1969 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Benarroch, D. / Egloff, M.P. / Mulard, L. / Romette, J.L. / Canard, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: A structural basis for the inhibition of the NS5 dengue virus mRNA 2'-O-methyltransferase domain by ribavirin 5'-triphosphate. Authors: Benarroch, D. / Egloff, M.P. / Mulard, L. / Guerreiro, C. / Romette, J.L. / Canard, B. #1: Journal: Embo J. / Year: 2002 Title: An RNA cap (nucleoside-2'-O-)-methyltransferase in the flavivirys RNA polymerase NS5:crystal structure and functional characterization Authors: EGLOFF, M.P. / BENARROCH, D. / SELISKO, B. / ROMETTE, J.L. / CANARD, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r6a.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r6a.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 1r6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/1r6a ftp://data.pdbj.org/pub/pdb/validation_reports/r6/1r6a | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33145.672 Da / Num. of mol.: 1 / Fragment: RNA-directed RNA polymerase (residue 2492-2784) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 Puerto Rico/PR159-S1/1969 Genus: Flavivirus / Species: Dengue virus / Strain: PR159-S1 / Gene: NS5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[pREP4] / References: UniProt: P12823, RNA-directed RNA polymerase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAH / | #4: Chemical | ChemComp-RVP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Na Citrate 0.1 M, AS 0.5 M, LiSO4 1.2 M, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 11869 / Num. obs: 11869 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rsym value: 0.067 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.6→2.73 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.273 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→25 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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