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Yorodumi- 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 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / DEMETHYLASE SPLICING CHROMATIN | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity ...positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / 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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / promoter-specific chromatin binding / HDACs deacetylate histones / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cerebral cortex development / transcription corepressor activity / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Toffolo, E. / Paganini, L. / Rusconi, F. / Tortorici, M. / Pilotto, S. / Verpelli, C. / Tedeschi, G. / Maffioli, E. / Sala, C. / Mattevi, A. / Battaglioli, E. | ||||||
Citation | Journal: J.Neurochem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bay.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bay.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/4bay ftp://data.pdbj.org/pub/pdb/validation_reports/ba/4bay | HTTPS FTP |
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-Related structure data
Related structure data | 2x0lS S: Starting model for refinement |
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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
#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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O60341, Oxidoreductases |
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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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UKL0 |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
Sequence details | MUTATION OF THREONINE 369B IN ASPARTATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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