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Yorodumi- PDB-7klr: Solution structure of the PHD1 domain of histone demethylase KDM5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7klr | |||||||||
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Title | Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide | |||||||||
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Keywords | GENE REGULATION / PHD / H3 / Epigenetics / KDM5A | |||||||||
Function / homology | Function and homology information [histone H3]-trimethyl-L-lysine4 demethylase / facultative heterochromatin formation / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / enzyme inhibitor activity / regulation of DNA-binding transcription factor activity / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization ...[histone H3]-trimethyl-L-lysine4 demethylase / facultative heterochromatin formation / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / enzyme inhibitor activity / regulation of DNA-binding transcription factor activity / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / 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 / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / circadian regulation of gene expression / 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 / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Longbotham, E.J. / Kelly, M.J.S. / Fujimori, D.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A. Authors: Longbotham, J.E. / Kelly, M.J.S. / Fujimori, D.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7klr.cif.gz | 414.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7klr.ent.gz | 355.6 KB | Display | PDB format |
PDBx/mmJSON format | 7klr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/7klr ftp://data.pdbj.org/pub/pdb/validation_reports/kl/7klr | HTTPS FTP |
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-Related structure data
Related structure data | 7kloC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6605.556 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KDM5A, JARID1A, RBBP2, RBP2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P29375, [histone H3]-trimethyl-L-lysine4 demethylase | ||
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#2: Protein/peptide | Mass: 1150.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J Production host: synthetic construct (others) / References: UniProt: P68431 | ||
#3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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