+Open data
-Basic information
Entry | Database: PDB / ID: 4qxc | ||||||
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Title | Crystal structure of histone demethylase KDM2A-H3K36ME2 with NOG | ||||||
Components |
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Keywords | Oxidoreductase/Structural Protein / cupin subfamily Fe(II)/2-OG dioxygenase / JmjC domain / Histone demethylase / Oxidoreductase-Structural Protein complex | ||||||
Function / homology | Function and homology information Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines ...Chromatin modifying enzymes / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / Interleukin-7 signaling / HDMs demethylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / neuroepithelial cell differentiation / unmethylated CpG binding / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / heart looping / histone demethylase activity / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / neural tube closure / transcription coregulator activity / circadian regulation of gene expression / multicellular organism growth / regulation of circadian rhythm / neuron differentiation / nucleosome assembly / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / gene expression / chromatin organization / in utero embryonic development / protein heterodimerization activity / negative regulation of gene expression / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Cheng, Z.J. / Patel, D.J. | ||||||
Citation | Journal: Genes Dev. / Year: 2014 Title: A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36. Authors: Cheng, Z. / Cheung, P. / Kuo, A.J. / Yukl, E.T. / Wilmot, C.M. / Gozani, O. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qxc.cif.gz | 184.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qxc.ent.gz | 151 KB | Display | PDB format |
PDBx/mmJSON format | 4qxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/4qxc ftp://data.pdbj.org/pub/pdb/validation_reports/qx/4qxc | HTTPS FTP |
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-Related structure data
Related structure data | 4qwnC 4qx7C 4qx8C 4qxbC 4qxhC 4tn7C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Lysine-specific demethylase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 39031.324 Da / Num. of mol.: 2 / Fragment: UNP residues 36-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: F6YRW4, UniProt: P59997*PLUS, [histone H3]-dimethyl-L-lysine36 demethylase #2: Protein | Mass: 7534.759 Da / Num. of mol.: 2 / Fragment: UNP residues 450-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm2a, Fbxl11, Jhdm1a, Kiaa1004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: F6YRW4, UniProt: P59997*PLUS, [histone H3]-dimethyl-L-lysine36 demethylase |
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-Protein/peptide , 1 types, 2 molecules EF
#3: Protein/peptide | Mass: 1666.967 Da / Num. of mol.: 2 / Fragment: UNP residues 30-44 / Source method: obtained synthetically / Details: mono-methylated H3 peptide was synthesized / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P84228 |
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-Non-polymers , 3 types, 450 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.1 Å3/Da / Density % sol: 41.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M CITRATE NA 18% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→86 Å / Num. all: 78516 / Num. obs: 77731 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.061 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.326 / Rsym value: 0.29 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→85.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.751 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.208 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→85.49 Å
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