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Yorodumi- PDB-3njy: Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyqui... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3njy | ||||||
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Title | Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyquinoline | ||||||
Components | Lysine-specific demethylase 4A | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE / CHROMATIN REGULATOR / TRANSCRIPTION REGULATION / DOUBLE-STRANDED BETA HELIX / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / negative regulation of autophagy / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | King, O.N.F. / Clifton, I.J. / Wang, M. / Maloney, D.J. / Jadhav, A. / Oppermann, U. / Heightman, T.D. / Simeonov, A. / McDonough, M.A. / Schofield, C.J. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors Authors: King, O.N.F. / Li, X.S. / Sakurai, M. / Kawamura, A. / Rose, N.R. / Ng, S.S. / Quinn, A.M. / Rai, G. / Mott, B.T. / Beswick, P. / Klose, R.J. / Oppermann, U. / Jadhav, A. / Heightman, T.D. / ...Authors: King, O.N.F. / Li, X.S. / Sakurai, M. / Kawamura, A. / Rose, N.R. / Ng, S.S. / Quinn, A.M. / Rai, G. / Mott, B.T. / Beswick, P. / Klose, R.J. / Oppermann, U. / Jadhav, A. / Heightman, T.D. / Maloney, D.J. / Schofield, C.J. / Simeonov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3njy.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3njy.ent.gz | 125.2 KB | Display | PDB format |
PDBx/mmJSON format | 3njy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/3njy ftp://data.pdbj.org/pub/pdb/validation_reports/nj/3njy | HTTPS FTP |
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-Related structure data
Related structure data | 2oq6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: Catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNIC28 Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: O75164, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M CITRATE, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2009 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→41.24 Å / Num. all: 26805 / Num. obs: 26805 / % possible obs: 99.04 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.44 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 9.4073 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OQ6 Resolution: 2.6→37.678 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.32 / Isotropic thermal model: Isotropic / σ(F): 0.4 / σ(I): 0 / Phase error: 21.39 / 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 / Bsol: 30.238 Å2 / ksol: 0.336 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.64 Å2 / Biso mean: 41.1763 Å2 / Biso min: 13.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→37.678 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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