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Yorodumi- PDB-6rll: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rll | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146 | ||||||
Components |
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Keywords | TRANSLOCASE / PRMT5 / MEP50 / LIGAND | ||||||
Function / homology | Function and homology information positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / epithelial cell proliferation involved in prostate gland development / histone arginine N-methyltransferase activity / methylosome / protein-arginine N-methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / : / endothelial cell activation / histone H3 methyltransferase activity / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / regulation of mitotic nuclear division / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / liver regeneration / methyltransferase activity / DNA-templated transcription termination / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Brown, D.G. / Robinson, C.M. / Pande, V. | ||||||
Citation | Journal: To Be Published Title: A chemical probe for the methyl transferase PRMT5 with a novel binding mode Authors: Brown, D.G. / Robinson, C.M. / Pandeet, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rll.cif.gz | 199.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rll.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 6rll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/6rll ftp://data.pdbj.org/pub/pdb/validation_reports/rl/6rll | HTTPS FTP |
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-Related structure data
Related structure data | 4gqbS 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: 73763.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: O14744, type II protein arginine methyltransferase |
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#2: Protein | Mass: 37586.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: Q9BQA1 |
#3: Chemical | ChemComp-K8H / ( |
#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 Å3/Da / Density % sol: 59.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20-30% PEG3350; 150mM Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91739 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91739 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→89.65 Å / Num. obs: 60395 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.22→2.31 Å / Num. unique obs: 6070 / CC1/2: 0.85 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GQB Resolution: 2.22→89.44 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.24 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.43 Å2 / Biso mean: 34.864 Å2 / Biso min: 18.44 Å2
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Refinement step | Cycle: final / Resolution: 2.22→89.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.278 Å / Total num. of bins used: 20
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