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Yorodumi- PDB-3emd: Wesselsbron virus Methyltransferase in complex with Sinefungin an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3emd | ||||||
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Title | Wesselsbron virus Methyltransferase in complex with Sinefungin and 7MeGpppA | ||||||
Components | methyltransferase | ||||||
Keywords | TRANSFERASE / Flavivirus / RNA capping / Methyltransferase / Guanylyltransferase / viral enzyme structure | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 / 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 JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 / 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 entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / 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 | Wesselsbron virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bollati, M. / Milani, M. / Ricagno, S. / Mastrangelo, E. / Bolognesi, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Recognition of RNA Cap in the Wesselsbron Virus NS5 Methyltransferase Domain: Implications for RNA-Capping Mechanisms in Flavivirus Authors: Bollati, M. / Milani, M. / Mastrangelo, E. / Ricagno, S. / Tedeschi, G. / Nonnis, S. / Decroly, E. / Selisko, B. / de Lamballerie, X. / Coutard, B. / Canard, B. / Bolognesi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3emd.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3emd.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 3emd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/3emd ftp://data.pdbj.org/pub/pdb/validation_reports/em/3emd | HTTPS FTP |
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-Related structure data
Related structure data | 3eldC 3eluSC 3elwC 3elyC 3embC 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: 34193.172 Da / Num. of mol.: 1 Fragment: NS5 N-terminal methyltransferase domain, UNP residues 2500-2791 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wesselsbron virus / Strain: SAH-177 99871-2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) pRos References: UniProt: C8XPB0, UniProt: D0VX01*PLUS, methyltransferase cap1 | ||||
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#2: Chemical | ChemComp-SFG / | ||||
#3: Chemical | ChemComp-GTA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE THIRD PHOSPHATE GROUP IS NOT VISIBLE IN THE STRUCTURE AS WELL AS THE ADENOSINE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 1mM Sinefungin, 1mM 7MeGpppA, 10% PEG 4000, pH 6.2, VAPOR DIFFUSION, SITTING 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 10, 2007 / Details: mirrors |
Radiation | Monochromator: Diamond (111) Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.37 Å / Num. all: 21485 / Num. obs: 20462 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3093 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3ELU Resolution: 2→32.21 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.172 / ESU R Free: 0.158 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.475 Å2
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Refinement step | Cycle: LAST / Resolution: 2→32.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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