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Yorodumi- PDB-7bo7: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bo7 | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437 | ||||||
Components |
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Keywords | TRANSLOCASE / complex inhibitor bound PRMT5 MEP50 | ||||||
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 / methyl-CpG binding / positive regulation of mRNA splicing, via spliceosome / : / endothelial cell activation / histone H3 methyltransferase activity / Cul4B-RING E3 ubiquitin ligase complex / regulation of mitotic nuclear division / histone methyltransferase complex / 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 / methyltransferase activity / liver regeneration / 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: 2.83 Å | ||||||
Authors | Brown, D. / Robinson, C. / Carr, K.H. / Pande, V. | ||||||
Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437 Authors: Brown, D. / Robinson, C. / Carr, K.H. / Pande, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bo7.cif.gz | 372.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bo7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7bo7 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7bo7 | HTTPS FTP |
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-Related structure data
Related structure data | 6rlqS 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
-Protein , 2 types, 2 molecules AAABBB
#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 |
-Non-polymers , 5 types, 58 molecules
#3: Chemical | ChemComp-U6K / ( | ||||
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#4: Chemical | ChemComp-EPE / | ||||
#5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 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: 0.91741 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→60.367 Å / Num. obs: 30068 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.992 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.83→2.98 Å / Rmerge(I) obs: 1.379 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4286 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RLQ Resolution: 2.83→60.367 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.169 / SU B: 22.28 / SU ML: 0.382 / Average fsc free: 0.8639 / Average fsc work: 0.825 / Cross valid method: FREE R-VALUE / ESU R Free: 0.365 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.138 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→60.367 Å
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Refine LS restraints |
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LS refinement shell |
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