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Yorodumi- PDB-2v1d: Structural basis of LSD1-CoREST selectivity in histone H3 recognition -
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-Basic information
Entry | Database: PDB / ID: 2v1d | ||||||
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Title | Structural basis of LSD1-CoREST selectivity in histone H3 recognition | ||||||
Components |
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Keywords | OXIDOREDUCTASE/REPRESSOR / OXIDOREDUCTASE REPRESSOR COMPLEX / ALTERNATIVE SPLICING / OXIDOREDUCTASE / FLAVIN / REPRESSOR / TRANSCRIPTION REGULATION / CHROMATIN REMODELLING / HOST-VIRUS INTERACTION / NUCLEAR PROTEIN / PHOSPHORYLATION / CHROMATIN REGULATOR / OXIDOREDUCTASE-REPRESSOR complex | ||||||
Function / homology | Function and homology information 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 / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of epithelial to mesenchymal transition / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to cAMP / response to fungicide / Meiotic synapsis / Inhibition of DNA recombination at telomere / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of PTEN gene transcription / transcription repressor complex / Condensation of Prophase Chromosomes / erythrocyte differentiation / nuclear receptor coactivator activity / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / positive regulation of protein ubiquitination / negative regulation of protein binding / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / promoter-specific chromatin binding / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of DNA-binding transcription factor activity / p53 binding / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / structural constituent of chromatin / transcription corepressor activity / regulation of protein localization / cellular response to UV / nucleosome / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / positive regulation of cold-induced thermogenesis / flavin adenine dinucleotide binding / chromosome, telomeric region / DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / oxidoreductase activity / chromatin remodeling / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / 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 | Forneris, F. / Binda, C. / Adamo, A. / Battaglioli, E. / Mattevi, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural Basis of Lsd1-Corest Selectivity in Histone H3 Recognition. Authors: Forneris, F. / Binda, C. / Adamo, A. / Battaglioli, E. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v1d.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1d.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v1d_validation.pdf.gz | 763.3 KB | Display | wwPDB validaton report |
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Full document | 2v1d_full_validation.pdf.gz | 790 KB | Display | |
Data in XML | 2v1d_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 2v1d_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1d ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1d | HTTPS FTP |
-Related structure data
Related structure data | 2iw5S 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: 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: 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: 2263.666 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-22 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16695 | ||
#4: Chemical | ChemComp-FAD / | ||
Compound details | ENGINEEREDSequence details | TRUNCATED MUTANT LACKING THE FIRST 122 N-TERMINAL RESIDUES TRUNCATED MUTANT LACKING THE FIRST 304 N- ...TRUNCATED MUTANT LACKING THE FIRST 122 N-TERMINAL RESIDUES TRUNCATED MUTANT LACKING THE FIRST 304 N-TERMINAL RESIDUES SYNTHETIC PEPTIDE CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 7 Å3/Da / Density % sol: 80 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 44088 / % possible obs: 96 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.9 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IW5 Resolution: 3.1→76.03 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.687 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.293 / 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: 84.85 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→76.03 Å
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