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Yorodumi- PDB-3abu: Crystal Structure of LSD1 in complex with a 2-PCPA derivative, S1201 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3abu | ||||||
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Title | Crystal Structure of LSD1 in complex with a 2-PCPA derivative, S1201 | ||||||
Components | Lysine-specific histone demethylase 1 | ||||||
Keywords | OXIDOREDUCTASE / Amine Oxidase / Histone demethylase / Tower domain / H3K4 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Chromatin regulator / Developmental protein / FAD / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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 / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / 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 / 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: 3.1 Å | ||||||
Authors | Mimasu, S. / Umezawa, N. / Sato, S. / Higuchi, T. / Umehara, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structurally Designed trans-2-Phenylcyclopropylamine Derivatives Potently Inhibit Histone Demethylase LSD1/KDM1 Authors: Mimasu, S. / Umezawa, N. / Sato, S. / Higuchi, T. / Umehara, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3abu.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3abu.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 3abu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/3abu ftp://data.pdbj.org/pub/pdb/validation_reports/ab/3abu | HTTPS FTP |
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-Related structure data
Related structure data | 3abtC 2dw4S 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
#1: Protein | Mass: 73652.242 Da / Num. of mol.: 1 Fragment: amine oxidase (flavin containing) domain 2, residues 172-833 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Kazusa DNA KIAA 0601 / Plasmid: pGEX-6P-Hs / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: O60341 |
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#2: Chemical | ChemComp-12F / [( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.95 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3-10% PEG 2000 Monomethyl ether, 0.1M Hepes pH 7.5, 0.2M magnesium chloride, 0.1M cacodylate, 5mM Tranylcypromine-derivative, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3.1→50 Å / Num. all: 22251 / Num. obs: 20212 / % possible obs: 99.9 % / Redundancy: 18.08 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 19.38 | ||||||||||||||||||
Reflection shell | Resolution: 3.09→3.16 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 5.13 / Num. unique all: 1562 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2dw4 Resolution: 3.1→47.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 74039.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 5.1 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 14.1333 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→47.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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