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Yorodumi- PDB-3gdh: Methyltransferase domain of human Trimethylguanosine Synthase 1 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gdh | ||||||
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Title | Methyltransferase domain of human Trimethylguanosine Synthase 1 (TGS1) bound to m7GTP and adenosyl-homocysteine (active form) | ||||||
Components | Trimethylguanosine synthase homolog | ||||||
Keywords | TRANSFERASE / m7G / cap / dimethyltransferase / UsnRNA / snoRNA / telomerase / Cytoplasm / Methyltransferase / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information ribonucleoprotein complex biogenesis / RNA cap trimethylguanosine synthase activity / 7-methylguanosine RNA capping / RNA methyltransferase activity / 7-methylguanosine cap hypermethylation / small nuclear ribonucleoprotein complex / Cajal body / spliceosomal snRNP assembly / RORA activates gene expression / Transferases; Transferring one-carbon groups; Methyltransferases ...ribonucleoprotein complex biogenesis / RNA cap trimethylguanosine synthase activity / 7-methylguanosine RNA capping / RNA methyltransferase activity / 7-methylguanosine cap hypermethylation / small nuclear ribonucleoprotein complex / Cajal body / spliceosomal snRNP assembly / RORA activates gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / snRNP Assembly / nucleolus / extracellular space / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Monecke, T. / Dickmanns, A. / Ficner, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1. Authors: Monecke, T. / Dickmanns, A. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gdh.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gdh.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/3gdh ftp://data.pdbj.org/pub/pdb/validation_reports/gd/3gdh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 26743.785 Da / Num. of mol.: 3 / Fragment: UNP residues 618-853 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGS1, HCA137, NCOA6IP, PIMT / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96RS0, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 5 types, 420 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGR / #5: Chemical | ChemComp-PGO / | #6: 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: 2.94 Å3/Da / Density % sol: 58.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: PEG 8000, pH 6, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2008 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. obs: 61489 / % possible obs: 99.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.464 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2→30 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 1.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.39 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell |
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