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Yorodumi- PDB-3evg: Crystal structure of Dengue-2 virus methyltransferase complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3evg | ||||||
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Title | Crystal structure of Dengue-2 virus methyltransferase complexed with S-adenosyl-L-homocysteine | ||||||
Components | RNA-directed RNA polymerase NS5 | ||||||
Keywords | TRANSFERASE / Dengue virus / Flavivirus / NS5 Methyltransferase / RNA cap binding / ATP-binding / Capsid protein / Cleavage on pair of basic residues / Endoplasmic reticulum / Envelope protein / Glycoprotein / Helicase / Hydrolase / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribonucleoprotein / RNA replication / RNA-binding / RNA-directed RNA polymerase / Secreted / Serine protease / Transcription / Transcription regulation / Transmembrane / Viral nucleoprotein / Virion | ||||||
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 16681-PDK53 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Thompson, A.A. / Geiss, B.J. / Peersen, O.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Analysis of flavivirus NS5 methyltransferase cap binding. Authors: Geiss, B.J. / Thompson, A.A. / Andrews, A.J. / Sons, R.L. / Gari, H.H. / Keenan, S.M. / Peersen, O.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3evg.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3evg.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3evg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/3evg ftp://data.pdbj.org/pub/pdb/validation_reports/ev/3evg | HTTPS FTP |
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-Related structure data
Related structure data | 3evaC 3evbC 3evcC 3evdC 3eveC 3evfC 1l9kS 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: 30836.152 Da / Num. of mol.: 1 Fragment: N-terminal domain 1-267 of RNA-directed RNA polymerase NS5: UNP residues 2493-2757 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 16681-PDK53 / Strain: 16681 / Plasmid: pKKT7E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS References: UniProt: P29991, mRNA (guanine-N7)-methyltransferase, RNA-directed RNA polymerase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAH / | #4: 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: 3.31 Å3/Da / Density % sol: 62.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2 M Ammonium sulfate, 0.65 M Lithium sulfate, 0.1 M Sodium citrate pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28 Å / Num. obs: 39142 / % possible obs: 97.8 % / Redundancy: 6.69 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.099 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.35 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.439 / % possible all: 95.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L9K Resolution: 2.2→27 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing and refinement
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Displacement parameters | Biso mean: 45.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→27 Å
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Refine LS restraints |
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