+Open data
-Basic information
Entry | Database: PDB / ID: 5x60 | ||||||
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Title | Crystal structure of LSD1-CoREST in complex with peptide 9 | ||||||
Components |
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Keywords | OXIDOREDUCTASE/TRANSCRIPTION / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / COREPRESSOR / OXIDOREDUCTASE-TRANSCRIPTION complex | ||||||
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / erythrocyte differentiation / DNA methylation / Condensation of Prophase Chromosomes / nuclear receptor coactivator activity / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / negative regulation of protein binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / cellular response to gamma radiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cerebral cortex development / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / 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 / cellular response to UV / regulation of protein localization / nucleosome / p53 binding / flavin adenine dinucleotide binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cold-induced thermogenesis / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / 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 / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Kikuchi, M. / Amano, Y. / Sato, S. / Yokoyama, S. / Umezawa, N. / Higuchi, T. / Umehara, T. | ||||||
Citation | Journal: Bioorg. Med. Chem. / Year: 2017 Title: Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1. Authors: Amano, Y. / Kikuchi, M. / Sato, S. / Yokoyama, S. / Umehara, T. / Umezawa, N. / Higuchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x60.cif.gz | 178.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x60.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x60 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x60 | HTTPS FTP |
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-Related structure data
Related structure data | 5h6qC 5h6rC 2v1dS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 74333.039 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 172-833 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O60341, Oxidoreductases |
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#2: Protein | Mass: 15850.929 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 311-443 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q9UKL0 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2208.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS |
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-Non-polymers , 3 types, 64 molecules
#4: Chemical | ChemComp-FAD / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.94 Å3/Da / Density % sol: 82.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M N-(2-acetamido)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→50 Å / Num. obs: 71152 / % possible obs: 99.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.68→2.73 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3551 / CC1/2: 0.887 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V1D Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.345 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.196 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.272 Å2
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Refinement step | Cycle: 1 / Resolution: 2.69→50 Å
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