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Yorodumi- PDB-4lxl: Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lxl | ||||||
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Title | Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3 | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PEPTIDE / JmjC domain / Demethylation / Histone / Methylation / Nucleus / OXIDOREDUCTASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling ...histone H3K36 demethylase activity / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone demethylase activity / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / brain development / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / HATs acetylate histones / gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) human (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Wang, W.-C. / Chu, C.-H. / Chen, C.-C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3 Authors: Wang, W.-C. / Chu, C.-H. / Chen, C.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lxl.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lxl.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 4lxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lxl_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 4lxl_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 4lxl_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4lxl_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/4lxl ftp://data.pdbj.org/pub/pdb/validation_reports/lx/4lxl | HTTPS FTP |
-Related structure data
Related structure data | 2ybsS 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 / Protein/peptide , 2 types, 2 molecules AD
#1: Protein | Mass: 42419.105 Da / Num. of mol.: 1 / Fragment: Catalytic domain, UNP RESIDUES 1-348 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4B / Production host: Escherichia coli (E. coli) References: UniProt: O94953, 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: 849.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) human (human) / References: UniProt: P68431*PLUS |
-Non-polymers , 4 types, 265 molecules
#3: Chemical | ChemComp-PD2 / |
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#4: Chemical | ChemComp-NI / |
#5: Chemical | ChemComp-ZN / |
#6: 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: 2.1 Å3/Da / Density % sol: 41.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24% PEG8000, 0.2M magnesium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: May 22, 2013 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→30 Å / Num. all: 30463 / Num. obs: 30173 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.368 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YBS Resolution: 1.87→28.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.905 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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 max: 94.17 Å2 / Biso mean: 26.5967 Å2 / Biso min: 10.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→28.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
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