+Open data
-Basic information
Entry | Database: PDB / ID: 5emk | ||||||
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Title | Crystal structure of PRMT5:MEP50 with Compound 9 and sinefungin | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein-inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / Resolution: 2.52 Å | ||||||
Authors | Boriack-Sjodin, P.A. / Jin, L. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2016 Title: Structure and Property Guided Design in the Identification of PRMT5 Tool Compound EPZ015666. Authors: Duncan, K.W. / Rioux, N. / Boriack-Sjodin, P.A. / Munchhof, M.J. / Reiter, L.A. / Majer, C.R. / Jin, L. / Johnston, L.D. / Chan-Penebre, E. / Kuplast, K.G. / Porter Scott, M. / Pollock, R.M. ...Authors: Duncan, K.W. / Rioux, N. / Boriack-Sjodin, P.A. / Munchhof, M.J. / Reiter, L.A. / Majer, C.R. / Jin, L. / Johnston, L.D. / Chan-Penebre, E. / Kuplast, K.G. / Porter Scott, M. / Pollock, R.M. / Waters, N.J. / Smith, J.J. / Moyer, M.P. / Copeland, R.A. / Chesworth, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5emk.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5emk.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 5emk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/5emk ftp://data.pdbj.org/pub/pdb/validation_reports/em/5emk | HTTPS FTP |
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-Related 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 AB
#1: Protein | Mass: 73763.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: coexpressed with MEP50 / Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Plasmid: pDEST / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O14744, Transferases; Transferring one-carbon groups; Methyltransferases, EC: 2.1.1.125 |
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#2: Protein | Mass: 37862.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: coexpressed with PRMT5 / Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Plasmid: pDEST / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BQA1 |
-Non-polymers , 4 types, 82 molecules
#3: Chemical | ChemComp-SFG / | ||
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#4: Chemical | ChemComp-5QH / ~{ | ||
#5: Chemical | #6: 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: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07816 Å | |||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 3, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07816 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.52→54.63 Å / Num. obs: 42869 / % possible obs: 99.4 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.025 / Net I/σ(I): 19.4 / Num. measured all: 239412 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Resolution: 2.52→54.49 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.727 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 207.81 Å2 / Biso mean: 63.971 Å2 / Biso min: 18.47 Å2
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Refinement step | Cycle: final / Resolution: 2.52→54.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.585 Å / Total num. of bins used: 20
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