+Open data
-Basic information
Entry | Database: PDB / ID: 8q1h | ||||||
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Title | LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Histone Code / Demethylase / Flavin | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / positive regulation of neural precursor cell proliferation / neuron maturation / 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 / nucleosomal DNA binding / histone demethylase activity / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / euchromatin / 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 / cerebral cortex development / positive regulation of neuron projection development / structural constituent of chromatin / transcription corepressor activity / cellular response to UV / regulation of protein localization / nucleosome / p53 binding / flavin adenine dinucleotide binding / positive regulation of cold-induced thermogenesis / chromatin organization / Factors involved in megakaryocyte development and platelet production / positive regulation of cell growth / 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 / protein heterodimerization 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: 2.9 Å | ||||||
Authors | Barone, M. / Mattevi, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: To Be Published Title: Uncoupling Histone Modification Crosstalk by Engineering Lysine Demethylase LSD1 Authors: Kwangwoon, L. / Barone, M. / Waterbury, A.L. / Jiang, H. / Nam, E. / Whedon, S.D. / Wang, Z.A. / Caroli, J. / Ibeabuchi, B. / Neal, K. / Dhoondia, Z. / Kuroda, M. / Liau, B. / Beck, S. / Mattevi, A. / Cole, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q1h.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q1h.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 8q1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/8q1h ftp://data.pdbj.org/pub/pdb/validation_reports/q1/8q1h | HTTPS FTP |
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-Related structure data
Related structure data | 8q1gC 8q1jC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 81245.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O60341 |
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#2: Protein | Mass: 20244.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UKL0 |
#3: Protein/peptide | Mass: 2263.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2 |
#4: Chemical | ChemComp-FAD / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.95 Å3/Da / Density % sol: 79.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium Tartrate 1.2 M, ADA 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.86 Å / Num. obs: 54837 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.072 / Rrim(I) all: 0.152 / Χ2: 1.01 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.9→2.98 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.786 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4461 / CC1/2: 0.383 / Rpim(I) all: 0.972 / Rrim(I) all: 2.043 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.86 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.86 Å
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Refine LS restraints |
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LS refinement shell |
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