+Open data
-Basic information
Entry | Database: PDB / ID: 7kib | ||||||
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Title | PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / 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 / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / methylosome / protein-arginine N-methyltransferase activity / 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 / 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 / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Palte, R.L. / Hayes, R.P. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kib.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kib.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 7kib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kib_validation.pdf.gz | 754.6 KB | Display | wwPDB validaton report |
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Full document | 7kib_full_validation.pdf.gz | 764.4 KB | Display | |
Data in XML | 7kib_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 7kib_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/7kib ftp://data.pdbj.org/pub/pdb/validation_reports/ki/7kib | HTTPS FTP |
-Related structure data
Related structure data | 7kicC 7kidC 6uxxS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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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 Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Trichoplusia ni (cabbage looper) 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.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BQA1 |
-Non-polymers , 5 types, 440 molecules
#3: Chemical | ChemComp-WFM / ( | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | #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: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→46.55 Å / Num. obs: 43599 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.52→2.62 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4503 / CC1/2: 0.932 / Rpim(I) all: 0.29 / Rrim(I) all: 0.664 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UXX Resolution: 2.52→46.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.419 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.263
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Displacement parameters | Biso max: 156.7 Å2 / Biso mean: 66.74 Å2 / Biso min: 30.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.52→46.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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