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Yorodumi- PDB-6e86: Solution structure of ZZZ3 ZZ domain in complex with histone H3K4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+86 | |||||||||
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Title | Solution structure of ZZZ3 ZZ domain in complex with histone H3K4ac peptide | |||||||||
Components |
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Keywords | GENE REGULATION / ZZZ3 / ZZ domain / histone / chromatin | |||||||||
Function / homology | Function and homology information ATAC complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / histone reader activity ...ATAC complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / histone reader activity / 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 / lysine-acetylated histone binding / 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 / mitotic spindle / 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 / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / nucleolus / regulation of DNA-templated transcription / 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 | Zhang, Y. / Kutateladze, T.G. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation. Authors: Mi, W. / Zhang, Y. / Lyu, J. / Wang, X. / Tong, Q. / Peng, D. / Xue, Y. / Tencer, A.H. / Wen, H. / Li, W. / Kutateladze, T.G. / Shi, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e86.cif.gz | 437 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e86.ent.gz | 363.5 KB | Display | PDB format |
PDBx/mmJSON format | 6e86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e86 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e86 | HTTPS FTP |
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-Related structure data
Related structure data | 6e83C 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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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7279.126 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZZZ3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYH5 |
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#2: Protein/peptide | Mass: 975.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2 mM [U-13C; U-15N] ZZ domain of ZZZ3, 4 nM H3K4ac, 7 % [U-99% 2H] D2O, 90% H2O/10% D2O Details: 20mM Tris (pH7.0), 100mM NaCl, 5mM DTT, 7% D2O / Label: 13C/15N / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |