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Open data
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Basic information
Entry | Database: PDB / ID: 4xbf | ||||||
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Title | Structure of LSD1:CoREST in complex with ssRNA | ||||||
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![]() | Oxidoreductase/Transcription/RNA / LSD1 / lysine specific demethylase / demethylase / demethylation / RNA / CoREST / REST Co-repressor 1 / amine oxidase / coiled-coil / SWIRM / chromatin remodelling enzyme / epigenetics / histone modifying enzyme / non-coding RNA / ncRNA / KDM1A / Oxidoreductase-Transcription-RNA complex | ||||||
Function / homology | ![]() 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 / positive regulation of epithelial to mesenchymal transition / 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 / HDACs deacetylate histones / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / oxidoreductase activity / transcription coactivator activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luka, Z. / Loukachevitch, L.V. / Martin, W.J. / Wagner, C. / Reiter, N.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme. Authors: Hirschi, A. / Martin, W.J. / Luka, Z. / Loukachevitch, L.V. / Reiter, N.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.9 KB | Display | ![]() |
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PDB format | ![]() | 256.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805.3 KB | Display | ![]() |
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Full document | ![]() | 811.5 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iw5S S: Starting model for refinement |
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Similar structure data |
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Links
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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: UNP residues 171-836 Source method: isolated from a genetically manipulated source Details: recombinant plasmid (residues 171-852) / Source: (gene. exp.) ![]() Details (production host): MJ23, N-terminal 6X HIS-tag expression vector Production host: ![]() ![]() |
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#2: Protein | Mass: 15317.435 Da / Num. of mol.: 1 / Fragment: UNP residues 308-440 Source method: isolated from a genetically manipulated source Details: amino acids residues 286-482, gift from Dr. Phillip Cole. Source: (gene. exp.) ![]() ![]() ![]() |
-RNA chain , 1 types, 1 molecules D
#3: RNA chain | Mass: 1586.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 30 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-FAD / | ||||
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#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density % sol: 80 % / Description: orthorhombic I222 space group |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, ...Details: The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT] PH range: 5.6-6.4 / Temp details: room temp |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen stream |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2014 Details: 12.7 KeV energy range, focused beam size: 50uM x 50uM |
Radiation | Monochromator: Diamond (C111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.803→49.018 Å / Num. all: 62563 / Num. obs: 62270 / % possible obs: 99.5 % / Redundancy: 14.6 % / Rsym value: 0.037 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.803→2.8732 Å / Redundancy: 12.5 % / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IW5 Resolution: 2.803→49.018 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.42 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.803→49.018 Å
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Refine LS restraints |
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LS refinement shell |
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