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Yorodumi- PDB-4r8r: Dengue virus serotype 3 methyltransferase without a bound S-adeno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r8r | ||||||
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Title | Dengue virus serotype 3 methyltransferase without a bound S-adenosyl methionine | ||||||
Components | nonstructural protein NS5 | ||||||
Keywords | TRANSFERASE / N7 methyltransferase / 2'O methyltransferase | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / serine-type endopeptidase activity / 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 / virion attachment to host cell / structural molecule activity / virion membrane / 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: 1.46 Å | ||||||
Authors | Noble, C.G. | ||||||
Citation | Journal: Antiviral Res. / Year: 2014 Title: Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine Authors: Noble, C.G. / Li, S.H. / Dong, H. / Chew, S.H. / 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 | 4r8r.cif.gz | 132.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r8r.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/4r8r ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r8r | HTTPS FTP |
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-Related structure data
Related structure data | 4r8sC 3p97S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30069.586 Da / Num. of mol.: 2 / Fragment: N-terminal domain, UNP residues 2491-2752 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 3 / Production host: Escherichia coli (E. coli) References: UniProt: C1KBQ3, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1 #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: 2.41 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22.5% PEG 8000, 0.2M NaCl, 0.1M Tris-HCl, 20mM tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→61.09 Å / Num. all: 97696 / Num. obs: 97614 / % possible obs: 96.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.94 Å2 |
Reflection shell | Resolution: 1.46→1.6 Å / % possible all: 94.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P97 Resolution: 1.46→57.93 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.9456 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.072
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Displacement parameters | Biso max: 95.46 Å2 / Biso mean: 22.55 Å2 / Biso min: 6.23 Å2
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Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→57.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.5 Å / Total num. of bins used: 20
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