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Yorodumi- PDB-7zup: Human PRMT5:MEP50 structure with Fragment (Example 18) and MTA Bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zup | ||||||
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Title | Human PRMT5:MEP50 structure with Fragment (Example 18) and MTA Bound | ||||||
Components |
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Keywords | TRANSFERASE / MTAP / methyl transferase / fragment-based lead discovery / FBDD | ||||||
Function / homology | Function and homology information positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / peptidyl-arginine methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / 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 / peptidyl-arginine methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / 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 / 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 / histone methyltransferase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / ribonucleoprotein complex binding / spliceosomal snRNP assembly / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Ahmad, M.U. / Koelmel, W. / Arkhipova, V. / Lawson, J.D. / Smith, C.R. / Gunn, R.J. | ||||||
Funding support | 1items
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Citation | Journal: Rsc Med Chem / Year: 2022 Title: Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits. Authors: Smith, C.R. / Kulyk, S. / Ahmad, M.U.D. / Arkhipova, V. / Christensen, J.G. / Gunn, R.J. / Ivetac, A. / Ketcham, J.M. / Kuehler, J. / Lawson, J.D. / Thomas, N.C. / Wang, X. / Marx, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zup.cif.gz | 207.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zup.ent.gz | 159.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zup_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 7zup_full_validation.pdf.gz | 492.9 KB | Display | |
Data in XML | 7zup_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 7zup_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/7zup ftp://data.pdbj.org/pub/pdb/validation_reports/zu/7zup | HTTPS FTP |
-Related structure data
Related structure data | 7uy1C 7uyfC 7zuqC 7zuuC 7zuyC 7zv2C 7zvlC 7zvuC 8csgC 8ctbC 5emlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Spodoptera frugiperda (fall armyworm) 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BQA1 |
-Non-polymers , 4 types, 221 molecules
#3: Chemical | ChemComp-MTA / | ||
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#4: Chemical | ChemComp-JYX / | ||
#5: Chemical | #6: 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: 2.9 Å3/Da / Density % sol: 57.53 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 15% PEG3350, 100 mM Na citrate, pH 5.4, 100mM Carboxylic acids |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9197 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→109.59 Å / Num. obs: 39692 / % possible obs: 93.25 % / Observed criterion σ(I): 1.9 / Redundancy: 11.9 % / CC1/2: 0.99 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.97→2.26 Å / Num. unique obs: 1985 / CC1/2: 0.77 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EML Resolution: 2.01→109.59 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.25 Å2 / Biso mean: 30.724 Å2 / Biso min: 13.09 Å2
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Refinement step | Cycle: final / Resolution: 2.01→109.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.012→2.064 Å / Total num. of bins used: 20
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