+Open data
-Basic information
Entry | Database: PDB / ID: 2ejr | ||||||
---|---|---|---|---|---|---|---|
Title | LSD1-tranylcypromine complex | ||||||
Components | Lysine-specific histone demethylase 1 | ||||||
Keywords | OXIDOREDUCTASE / Tower domain / LSD1 / FAD / Tranylcypromine / Parnate / amine oxidase / histone / demethylase / Alternative splicing / Chromatin regulator / Coiled coil / Nucleus / Phosphorylation / Repressor / Transcription / Transcription regulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
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: 2.7 Å | ||||||
Authors | Sengoku, T. / Mimasu, S. / Umehara, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: Crystal structure of histone demethylase LSD1 and tranylcypromine at 2.25A Authors: Mimasu, S. / Sengoku, T. / Fukuzawa, S. / Umehara, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ejr.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ejr.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ejr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/2ejr ftp://data.pdbj.org/pub/pdb/validation_reports/ej/2ejr | HTTPS FTP |
---|
-Related structure data
Related structure data | 2dw4SC 2z3yC 2z5uC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 73652.242 Da / Num. of mol.: 1 / Fragment: LSD1, residues 172-833 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0601, LSD1 / Plasmid: p-GEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60341, Oxidoreductases |
---|---|
#2: Chemical | ChemComp-F2N / [( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.55 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.5-4% PEG 2000, 0.1M HEPES-Na, 5% MPD, 5mM Tranylcypromine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2006 / Details: mirrors |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.1 Å / Num. obs: 30564 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 19.7 % / Biso Wilson estimate: 66.8 Å2 / Rsym value: 0.133 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2765 / % possible all: 91.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DW4 Resolution: 2.7→48.1 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2694604.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.5857 Å2 / ksol: 0.304489 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→48.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|