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Yorodumi- PDB-2oqb: Crystal structure of the N-terminal domain of coactivator-associa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oqb | ||||||
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Title | Crystal structure of the N-terminal domain of coactivator-associated methyltransferase 1 (CARM1) | ||||||
Components | Histone-arginine methyltransferase CARM1 | ||||||
Keywords | TRANSFERASE / GENE REGULATION / Protein Arginine methyltransferase / transcriptional regulation / activation domain | ||||||
Function / homology | Function and homology information RMTs methylate histone arginines / Estrogen-dependent gene expression / Regulation of lipid metabolism by PPARalpha / histone H3R26 methyltransferase activity / Cytoprotection by HMOX1 / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / negative regulation of dendrite development ...RMTs methylate histone arginines / Estrogen-dependent gene expression / Regulation of lipid metabolism by PPARalpha / histone H3R26 methyltransferase activity / Cytoprotection by HMOX1 / regulation of growth plate cartilage chondrocyte proliferation / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / protein-arginine N-methyltransferase activity / replication fork reversal / positive regulation of epithelial cell apoptotic process / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / intracellular estrogen receptor signaling pathway / intracellular steroid hormone receptor signaling pathway / protein localization to chromatin / response to cAMP / RNA splicing / nuclear receptor coactivator activity / lysine-acetylated histone binding / mRNA processing / RNA polymerase II transcription regulator complex / methylation / DNA-binding transcription factor binding / cell population proliferation / transcription coactivator activity / transcription cis-regulatory region binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.69 Å | ||||||
Authors | Cavarelli, J. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. Authors: Troffer-Charlier, N. / Cura, V. / Hassenboehler, P. / Moras, D. / Cavarelli, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oqb.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oqb.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 2oqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/2oqb ftp://data.pdbj.org/pub/pdb/validation_reports/oq/2oqb | HTTPS FTP |
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-Related 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: 12848.558 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Carm1, Prmt4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4AE70, EC: 2.1.1.125 #2: Chemical | ChemComp-CL / | #3: 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: 2.09 Å3/Da / Density % sol: 41.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 13%-16% PEG 6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→41.92 Å / Num. obs: 25232 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.052 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 9.7 / Num. unique all: 2470 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.69→41.92 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.626 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.126 / 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: 18.639 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→41.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.737 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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