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Yorodumi- PDB-2y48: Crystal structure of LSD1-CoREST in complex with a N-terminal SNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y48 | ||||||
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Title | Crystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide | ||||||
Components |
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Keywords | OXIDOREDUCTASE / FLAVIN / HISTONE / REPRESSOR / TRANSCRIPTION REGULATION / CHROMATIN / NUCLEAR PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of megakaryocyte differentiation / trophoblast giant cell differentiation / heterochromatin organization ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / negative regulation of vitamin D biosynthetic process / Regulation of CDH11 gene transcription / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of megakaryocyte differentiation / trophoblast giant cell differentiation / heterochromatin organization / 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 / Epithelial-Mesenchymal Transition (EMT) during gastrulation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / aortic valve morphogenesis / DNA repair complex / regulation of bicellular tight junction assembly / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / hair follicle morphogenesis / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / roof of mouth development / positive regulation of stem cell proliferation / negative regulation of DNA binding / E-box 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 / mesoderm formation / histone demethylase activity / canonical Wnt signaling pathway / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / Notch signaling pathway / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / fibrillar center / osteoblast differentiation / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / cellular response to UV / regulation of protein localization / sequence-specific double-stranded DNA binding / 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 / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Baron, R. / Binda, C. / Tortorici, M. / McCammon, J.A. / Mattevi, A. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Molecular Mimicry and Ligand Recognition in Binding and Catalysis by the Histone Demethylase Lsd1-Corest Complex. Authors: Baron, R. / Binda, C. / Tortorici, M. / Mccammon, J.A. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y48.cif.gz | 176.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y48.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 2y48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/2y48 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/2y48 | HTTPS FTP |
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-Related structure data
Related structure data | 2v1dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 81279.438 Da / Num. of mol.: 1 / Fragment: RESIDUES 123-852 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60341, Oxidoreductases |
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#2: Protein | Mass: 20244.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 305-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UKL0 |
#3: Protein/peptide | Mass: 2392.692 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 20 AMINO ACIDS TAIL, RESIUDES 2-21 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O95863 |
#4: Chemical | ChemComp-FAD / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 7 Å3/Da / Density % sol: 80 % / Description: NONE |
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Crystal grow | Details: 1.2 M SODIUM/POTASSIUM TARTRATE, 100 MM ADA BUFFER PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 3→70 Å / Num. obs: 50937 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V1D Resolution: 3→71.77 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.871 / SU B: 12.084 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.266 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.004 Å2
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Refinement step | Cycle: LAST / Resolution: 3→71.77 Å
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