[English] 日本語
Yorodumi- PDB-2uxn: Structural Basis of Histone Demethylation by LSD1 Revealed by Sui... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uxn | ||||||
---|---|---|---|---|---|---|---|
Title | Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/TRANSCRIPTION REGULATOR / OXIDOREDUCTASE-TRANSCRIPTION REGULATOR COMPLEX / OXIDOREDUCTASE-REPRESSOR COMPLEX / HISTONE DEMETHYLASE / FAD / LSD1 / COREST / REPRESSOR / TRANSCRIPTION REGULATION / HOST-VIRUS INTERACTION / CHROMATIN DEMETHYLATION / NUCLEAR PROTEIN / PHOSPHORYLATION / CHROMATIN REGULATOR / NUCLEOSOMES / TRANSCRIPTION / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / 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 / histone demethylase activity / telomere organization / Chromatin modifying enzymes / positive regulation of epithelial to mesenchymal transition / cellular response to cAMP / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of PTEN gene transcription / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / transcription repressor complex / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / erythrocyte differentiation / PRC2 methylates histones and DNA / nuclear receptor coactivator activity / Defective pyroptosis / Meiotic recombination / positive regulation of protein ubiquitination / negative regulation of protein binding / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / negative regulation of DNA-binding transcription factor activity / p53 binding / cellular response to gamma radiation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / cerebral cortex development / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of neuron projection development / structural constituent of chromatin / transcription corepressor activity / regulation of protein localization / cellular response to UV / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cold-induced thermogenesis / HATs acetylate histones / flavin adenine dinucleotide binding / gene expression / chromosome, telomeric region / DNA-binding transcription factor binding / Potential therapeutics for SARS / transcription regulator complex / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / oxidoreductase activity / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.72 Å | ||||||
Authors | Yang, M. / Culhane, J.C. / Szewczuk, L.M. / Gocke, C.B. / Brautigam, C.A. / Tomchick, D.R. / Machius, M. / Cole, P.A. / Yu, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Structural Basis of Histone Demethylation by Lsd1 Revealed by Suicide Inactivation. Authors: Yang, M. / Culhane, J.C. / Szewczuk, L.M. / Gocke, C.B. / Brautigam, C.A. / Tomchick, D.R. / Machius, M. / Cole, P.A. / Yu, H. #1: Journal: Mol.Cell / Year: 2006 Title: Structural Basis for Corest-Dependent Demethylation of Nucleosomes by the Human Lsd1 Histone Demethylase Authors: Yang, M. / Gocke, C.B. / Luo, X. / Borek, D. / Tomchick, D.R. / Machius, M. / Otwinowski, Z. / Yu, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uxn.cif.gz | 171.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uxn.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 2uxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uxn_validation.pdf.gz | 780.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2uxn_full_validation.pdf.gz | 787 KB | Display | |
Data in XML | 2uxn_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 2uxn_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/2uxn ftp://data.pdbj.org/pub/pdb/validation_reports/ux/2uxn | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 74126.781 Da / Num. of mol.: 1 Fragment: SWIRM DOMAIN, AMINE OXIDASE DOMAIN AND LINKER, RESIDUES 171-836 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MJ23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O60341, Oxidoreductases |
---|---|
#2: Protein | Mass: 26425.729 Da / Num. of mol.: 1 Fragment: FRAGMENT OF SANT1, LINKER REGION AND SANT2 DOMAIN, RESIDUES 286-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MJ65 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UKL0 |
-Protein/peptide , 1 types, 1 molecules E
#3: Protein/peptide | Mass: 2316.749 Da / Num. of mol.: 1 Fragment: HISTONE H3-DERIVED SUICIDE INHIBITOR, RESIDUES 2-22 Source method: obtained synthetically Details: HISTONE H3 N-TERMINAL PEPTIDE (RESIDUES 1-21 ) WITH A PROPARGYL MOIETY AT LYSINE 4 COVALENTLY ATTACHED TO FAD AND SUBSEQUENTLY REDUCED USING SODIUM BOROHYDRIDE Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431 |
---|
-Non-polymers , 4 types, 55 molecules
#4: Chemical | ChemComp-FDA / | ||
---|---|---|---|
#5: Chemical | ChemComp-GOL / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE CONSTRUCT USED CONTAINS A LINKER: (MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGR) FROM THE CLONING ...THE CONSTRUCT USED CONTAINS A LINKER: (MGSSHHHHHH |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6 Å3/Da / Density % sol: 79.6 % |
---|---|
Crystal grow | pH: 5.6 Details: PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 |
Detector | Type: CUSTOM / Detector: CCD / Date: Dec 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97927 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→48.57 Å / Num. obs: 69440 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 81.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 2.69→2.71 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 98.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 2.72→49 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU B: 19.548 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|