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Yorodumi- PDB-5oy3: The structural basis of the histone demethylase KDM6B histone 3 l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oy3 | ||||||
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Title | The structural basis of the histone demethylase KDM6B histone 3 lysine 27 specificity | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Epigenetics / Histone demethylase / substrate complex | ||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / Chromatin modifying enzymes ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / Chromatin modifying enzymes / epigenetic regulation of gene expression / response to fungicide / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / response to activity / Defective pyroptosis / HDACs deacetylate histones / hippocampus development / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / chromatin DNA binding / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / beta-catenin binding / Pre-NOTCH Transcription and Translation / cellular response to hydrogen peroxide / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cold-induced thermogenesis / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.136 Å | ||||||
Authors | Jones, S.E. / Olsen, L. / Gajhede, M. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Structural Basis of Histone Demethylase KDM6B Histone 3 Lysine 27 Specificity. Authors: Jones, S.E. / Olsen, L. / Gajhede, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oy3.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oy3.ent.gz | 158.2 KB | Display | PDB format |
PDBx/mmJSON format | 5oy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/5oy3 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oy3 | HTTPS FTP |
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-Related structure data
Related structure data | 6f6dC 3avrS S: Starting model for refinement C: citing same article (ref.) |
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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 / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 57919.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM6B, JMJD3, KIAA0346 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O15054, 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 |
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#2: Protein/peptide | Mass: 1820.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS |
-Non-polymers , 6 types, 312 molecules
#3: Chemical | ChemComp-FE / | ||||
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#4: Chemical | ChemComp-ZN / | ||||
#5: Chemical | ChemComp-AKG / | ||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-TBU / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M TRIS pH 7.5, 15%(v/v) Tert-butanol, |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.136→48.726 Å / Num. all: 343768 / Num. obs: 31653 / % possible obs: 99.86 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.055 / Rrim(I) all: 0.182 / Net I/σ(I): 12.67 |
Reflection shell | Rmerge(I) obs: 1.397 / Num. measured obs: 33112 / Num. unique all: 2951 / Rpim(I) all: 0.43 / Rrim(I) all: 1.463 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AVR Resolution: 2.136→48.726 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.73 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.136→48.726 Å
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Refine LS restraints |
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LS refinement shell |
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