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Open data
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Basic information
Entry | Database: PDB / ID: 7kic | ||||||
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Title | PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 34 | ||||||
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![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / E-box binding / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / negative regulation of gene expression via chromosomal CpG island methylation / regulation of mitotic nuclear division / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / spliceosomal snRNP assembly / liver regeneration / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / DNA-templated transcription termination / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / p53 binding / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Palte, R.L. | ||||||
![]() | ![]() Title: The Discovery of Two Novel Classes of 5,5-Bicyclic Nucleoside-Derived PRMT5 Inhibitors for the Treatment of Cancer. Authors: Quiroz, R.V. / Reutershan, M.H. / Schneider, S.E. / Sloman, D. / Lacey, B.M. / Swalm, B.M. / Yeung, C.S. / Gibeau, C. / Spellman, D.S. / Rankic, D.A. / Chen, D. / Witter, D. / Linn, D. / ...Authors: Quiroz, R.V. / Reutershan, M.H. / Schneider, S.E. / Sloman, D. / Lacey, B.M. / Swalm, B.M. / Yeung, C.S. / Gibeau, C. / Spellman, D.S. / Rankic, D.A. / Chen, D. / Witter, D. / Linn, D. / Munsell, E. / Feng, G. / Xu, H. / Hughes, J.M.E. / Lim, J. / Sauri, J. / Geddes, K. / Wan, M. / Mansueto, M.S. / Follmer, N.E. / Fier, P.S. / Siliphaivanh, P. / Daublain, P. / Palte, R.L. / Hayes, R.P. / Lee, S. / Kawamura, S. / Silverman, S. / Sanyal, S. / Henderson, T.J. / Ye, Y. / Gao, Y. / Nicholson, B. / Machacek, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.1 KB | Display | ![]() |
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PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kibC ![]() 7kidC ![]() 6uxxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() References: UniProt: O14744, type II protein arginine methyltransferase | ||||||
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#2: Protein | Mass: 37862.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-WFS / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.32 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→55 Å / Num. obs: 47006 / % possible obs: 96.5 % / Redundancy: 6.5 % / CC1/2: 1 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.44→2.53 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3881 / CC1/2: 0.885 / % possible all: 80.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UXX Resolution: 2.43→35.58 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.864 / SU R Cruickshank DPI: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.383 / SU Rfree Blow DPI: 0.262 / SU Rfree Cruickshank DPI: 0.264
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Displacement parameters | Biso max: 149.93 Å2 / Biso mean: 45.31 Å2 / Biso min: 5.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.43→35.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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