+Open data
-Basic information
Entry | Database: PDB / ID: 4kum | ||||||
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Title | Structure of LSD1-CoREST-Tetrahydrofolate complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE/TRANSCRIPTION REGULATOR / Histone demethylase / Folate Binding / Chromatin / nucleosomes / OXIDOREDUCTASE-TRANSCRIPTION REGULATOR 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 ...: / 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 / transcription factor binding / 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 / viral process / 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 / blood coagulation / 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 / transcription cis-regulatory region binding / DNA-binding transcription factor 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: 3.05 Å | ||||||
Authors | Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Calcutt, M.W. / Newcomer, M.E. / Wagner, C. | ||||||
Citation | Journal: Protein Sci. / Year: 2014 Title: Crystal structure of the histone lysine specific demethylase LSD1 complexed with tetrahydrofolate. Authors: Luka, Z. / Pakhomova, S. / Loukachevitch, L.V. / Calcutt, M.W. / Newcomer, M.E. / Wagner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kum.cif.gz | 339.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kum.ent.gz | 276 KB | Display | PDB format |
PDBx/mmJSON format | 4kum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kum ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kum | HTTPS FTP |
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-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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 74126.781 Da / Num. of mol.: 1 / Fragment: SWIRM andFAD binding domains, residues 171-836 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AOF2, KDM1, KDM1A, KIAA0601, LSD1 / Plasmid: MJ23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O60341 |
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#2: Protein | Mass: 26425.729 Da / Num. of mol.: 1 / Fragment: UNP residues 289-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, hCG_24743 / Plasmid: MJ65 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: J3KN32, UniProt: Q9UKL0*PLUS |
-Non-polymers , 5 types, 23 molecules
#3: Chemical | ChemComp-FAD / |
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#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-THG / ( |
#6: Chemical | ChemComp-CL / |
#7: 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: 6.49 Å3/Da / Density % sol: 81.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 47051 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 91.1 Å2 / Rsym value: 0.13 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 4.1 % / Rsym value: 0.67 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IW5 Resolution: 3.05→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 24.576 / SU ML: 0.203 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.263 / 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: 90.845 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→40 Å
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