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Yorodumi- PDB-2p41: Crystal Structure of Dengue Methyltransferase in Complex with 7Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p41 | ||||||
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Title | Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG2'OMe and S-Adenosyl-L-homocysteine | ||||||
Components | type II methyltransferase | ||||||
Keywords | VIRAL PROTEIN / TRANSFERASE / VIZIER / Viral Enzymes Involved in Replication / Dengue virus methyltransferase / Structural Genomics / Marseilles Structural Genomics Program @ AFMB / MSGP | ||||||
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 ...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 / induction by virus of host autophagy / 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 / virion attachment to host cell / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Egloff, M.P. / Marseilles Structural Genomics Program @ AFMB (MSGP) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5 Authors: Egloff, M.P. / Decroly, E. / Malet, H. / Selisko, B. / Benarroch, D. / Ferron, F. / Canard, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p41.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p41.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2p41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p41 ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p41 | HTTPS FTP |
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-Related structure data
Related structure data | 2p3lC 2p3oC 2p3qC 2p40C 1l9kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34397.027 Da / Num. of mol.: 1 / Fragment: residues 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 / Genus: Flavivirus / Species: Dengue virus / Strain: type 2 New Guinea / Gene: NSP5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS References: UniProt: Q9WLZ8, UniProt: Q9WLZ5*PLUS, RNA-directed RNA polymerase |
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-Non-polymers , 6 types, 315 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-G1G / | #4: Chemical | ChemComp-SAH / | #5: Chemical | ChemComp-CIT / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | SEQUENCE DIFFERENCES BETWEEN THIS STRUCTURE AND UNP ENTRY Q9WLZ8_9FLAV REFLECT ACTUAL DIFFERENCES ...SEQUENCE DIFFERENCE |
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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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, 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 | Date: Dec 14, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→38.9 Å / Num. all: 35292 / Num. obs: 35115 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.71 Å2 / Rsym value: 0.034 / Net I/σ(I): 37.6 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 4976 / Rsym value: 0.215 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L9K Resolution: 1.801→36.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.11 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.058 Å2
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Refinement step | Cycle: LAST / Resolution: 1.801→36.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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