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Yorodumi- PDB-6e83: Solution structure of ZZZ3 ZZ domain in complex with histone H3 tail -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+83 | ||||||
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Title | Solution structure of ZZZ3 ZZ domain in complex with histone H3 tail | ||||||
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 / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / histone reader activity / telomere organization ...ATAC complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / histone reader activity / 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 / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / mitotic spindle / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / 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 / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / 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 | 6e83.cif.gz | 454.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e83.ent.gz | 380 KB | Display | PDB format |
PDBx/mmJSON format | 6e83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e83_validation.pdf.gz | 415.1 KB | Display | wwPDB validaton report |
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Full document | 6e83_full_validation.pdf.gz | 595 KB | Display | |
Data in XML | 6e83_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6e83_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/6e83 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/6e83 | HTTPS FTP |
-Related structure data
Related structure data | 6e86C 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: 1308.488 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 |
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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: 5 | ||||||||||||||||||
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 |