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- PDB-2x0l: Crystal structure of a neuro-specific splicing variant of human h... -
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Basic information
Entry | Database: PDB / ID: 2x0l | ||||||
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Title | Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1. | ||||||
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![]() | TRANSCRIPTION / REPRESSOR COMPLEX / CHROMATIN REMODELLING / AMINE OXIDASE / HOST-VIRUS INTERACTION / TRANSCRIPTION REGULATION / PHOSPHOPROTEIN / OXIDOREDUCTASE / NUCLEAR PROTEIN / CHROMATIN REGULATOR / DEVELOPMENTAL PROTEIN | ||||||
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 / Chromatin modifying enzymes / positive regulation of epithelial to mesenchymal transition / epigenetic regulation of gene expression / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / telomere organization / transcription repressor complex / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / erythrocyte differentiation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / nuclear receptor coactivator activity / PRC2 methylates histones and DNA / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / Defective pyroptosis / HDACs deacetylate histones / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / PKMTs methylate histone lysines / cerebral cortex development / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / positive regulation of neuron projection development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / regulation of protein localization / cellular response to UV / nucleosome / nucleosome assembly / p53 binding / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / flavin adenine dinucleotide binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / 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 / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zibetti, C. / Adamo, A. / Binda, C. / Forneris, F. / Verpelli, C. / Ginelli, E. / Mattevi, A. / Sala, C. / Battaglioli, E. | ||||||
![]() | ![]() Title: Alternative Splicing of the Histone Demethylase Lsd1/Kdm1 Contributes to the Modulation of Neurite Morphogenesis in the Mammalian Nervous System. Authors: Zibetti, C. / Adamo, A. / Binda, C. / Forneris, F. / Toffolo, E. / Verpelli, C. / Ginelli, E. / Mattevi, A. / Sala, C. / 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 | ![]() | 177.2 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 764.2 KB | Display | ![]() |
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Full document | ![]() | 783.3 KB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iw5S 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: 81723.945 Da / Num. of mol.: 1 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1664.928 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-17 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Chemical | ChemComp-FAD / |
Sequence details | SPLICING VARIANT FORM OF THE PROTEIN LSD1: BETWEEN RESIDUE 369 AND 370 OF CHAIN A THERE ARE 4 ...SPLICING VARIANT FORM OF THE PROTEIN LSD1: BETWEEN RESIDUE 369 AND 370 OF CHAIN A THERE ARE 4 ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.7 Å3/Da / Density % sol: 78 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→70 Å / Num. obs: 49397 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IW5 Resolution: 3→71.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.868 / SU B: 11.819 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 64.132 Å2
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Refinement step | Cycle: LAST / Resolution: 3→71.5 Å
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Refine LS restraints |
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