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- PDB-4bay: Phosphomimetic mutant of LSD1-8a splicing variant in complex with... -
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Basic information
Entry | Database: PDB / ID: 4bay | ||||||
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Title | Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST | ||||||
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![]() | OXIDOREDUCTASE / DEMETHYLASE SPLICING CHROMATIN | ||||||
Function / homology | ![]() positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / regulation of androgen receptor signaling pathway / MRF binding / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / oxidoreductase activity / transcription coactivator activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toffolo, E. / Paganini, L. / Rusconi, F. / Tortorici, M. / Pilotto, S. / Verpelli, C. / Tedeschi, G. / Maffioli, E. / Sala, C. / Mattevi, A. / Battaglioli, E. | ||||||
![]() | ![]() Title: Phosphorylation of Neuronal Lysine-Specific Demethylase 1Lsd1/Kdm1A Impairs Transcriptional Repression by Regulating Interaction with Corest and Histone Deacetylases Hdac1/2. Authors: Toffolo, E. / Rusconi, F. / Paganini, L. / Tortorici, M. / Pilotto, S. / Heise, C. / Verpelli, C. / Tedeschi, G. / Maffioli, E. / Sala, C. / Mattevi, A. / Battaglioli, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.2 KB | Display | ![]() |
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PDB format | ![]() | 134.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 745.5 KB | Display | ![]() |
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Full document | ![]() | 753 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x0lS S: Starting model for refinement |
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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
#1: Protein | Mass: 76220.109 Da / Num. of mol.: 1 / Fragment: RESIDUES 192-876 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 15317.435 Da / Num. of mol.: 1 / Fragment: RESIDUES 308-440 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
Sequence details | MUTATION OF THREONINE 369B IN ASPARTATE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.74 Å3/Da / Density % sol: 75 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20DEG BY HANGING-DROP VAPOR DIFFUSION METHOD BY MIXING EQUAL VOLUMES OF PROTEIN SAMPLES WITH RESERVOIR SOLUTIONS CONTAINING 1.2 M SODIUM/POTASSIUM TARTRATE AND 100 MM N-(2-ACETAMIDO)IMINODIACETIC ACID, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→65 Å / Num. obs: 44180 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X0L Resolution: 3.1→59.06 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.101 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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 mean: 80.106 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→59.06 Å
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