+Open data
-Basic information
Entry | Database: PDB / ID: 4xbf | ||||||
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Title | Structure of LSD1:CoREST in complex with ssRNA | ||||||
Components |
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Keywords | 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 | Function and homology information positive regulation of megakaryocyte differentiation / 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 megakaryocyte differentiation / 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 / histone deacetylase complex / 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 / 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 / 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 / transcription corepressor activity / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / positive regulation of cold-induced thermogenesis / chromatin organization / 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 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: 2.803 Å | ||||||
Authors | Luka, Z. / Loukachevitch, L.V. / Martin, W.J. / Wagner, C. / Reiter, N.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: RNA / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xbf.cif.gz | 317.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbf.ent.gz | 256.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbf ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbf | HTTPS FTP |
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-Related structure data
Related structure data | 2iw5S S: Starting model for refinement |
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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
-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.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: pGEX-6P1 Details (production host): MJ23, N-terminal 6X HIS-tag expression vector Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O60341, Oxidoreductases |
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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.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Plasmid: Pet28 / Details (production host): MJ65 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE) / References: UniProt: Q9UKL0 |
-RNA chain , 1 types, 1 molecules D
#3: RNA chain | Mass: 1586.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 30 molecules
#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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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