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Yorodumi- PDB-2mnz: NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mnz | ||||||
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Title | NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / KDM5B / PHD1 / H3K4 / demethylase / repression | ||||||
Function / homology | Function and homology information regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus ...regulation of estradiol secretion / mammary duct terminal end bud growth / uterus morphogenesis / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of mammary gland epithelial cell proliferation / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / lens fiber cell differentiation / histone H3K4 demethylase activity / cellular response to fibroblast growth factor stimulus / branching involved in mammary gland duct morphogenesis / single fertilization / histone demethylase activity / response to fungicide / cellular response to leukemia inhibitory factor / post-embryonic development / Chromatin modifications during the maternal to zygotic transition (MZT) / HDMs demethylate histones / transcription corepressor activity / rhythmic process / sequence-specific double-stranded DNA binding / histone binding / nucleic acid binding / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | fewest violations, model1 | ||||||
Authors | Zhang, Y. / Yang, H.R. / Guo, X. / Rong, N.Y. / Song, Y.J. / Xu, Y.W. / Lan, W.X. / Xu, Y.H. / Cao, C. | ||||||
Citation | Journal: Protein Cell / Year: 2014 Title: The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B. Authors: Zhang, Y. / Yang, H. / Guo, X. / Rong, N. / Song, Y. / Xu, Y. / Lan, W. / Zhang, X. / Liu, M. / Xu, Y. / Cao, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mnz.cif.gz | 388 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mnz.ent.gz | 321.9 KB | Display | PDB format |
PDBx/mmJSON format | 2mnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/2mnz ftp://data.pdbj.org/pub/pdb/validation_reports/mn/2mnz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6133.000 Da / Num. of mol.: 1 / Fragment: Zinc finger domain PHD1, residues 306-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5B / Production host: Escherichia coli (E. coli) References: UniProt: Q9UGL1, 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: 1150.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8-2 mM [U-99% 13C; U-99% 15N] entity_1-1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Units: mM / Component: entity_1-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] / Conc. range: 0.8-2 |
Sample conditions | Ionic strength: 0.1 / pH: 7.4 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software | Name: CNS / Developer: Brunger A. T. et.al. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR constraints | NOE constraints total: 1263 / NOE intraresidue total count: 445 / NOE long range total count: 236 / NOE medium range total count: 218 / NOE sequential total count: 214 / Hydrogen bond constraints total count: 2 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 53 / Protein psi angle constraints total count: 53 |
NMR representative | Selection criteria: fewest violations |
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 |