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基本情報
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タイトル | Nucleosome 1 of the 4x197 nucleosome array containing H1 | |||||||||
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![]() | Chromatin / Nucleosomes / Linker Histone / DNA BINDING PROTEIN | |||||||||
機能・相同性 | ![]() negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends ...negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / heterochromatin / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / 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 / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / 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 / euchromatin / heterochromatin formation / chromatin DNA binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / double-stranded DNA binding / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | |||||||||
![]() | Dombrowski M / Cramer P | |||||||||
資金援助 | European Union, 1件
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![]() | ![]() タイトル: Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. 著者: Marco Dombrowski / Maik Engeholm / Christian Dienemann / Svetlana Dodonova / Patrick Cramer / ![]() 要旨: Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM ...Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions. | |||||||||
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マップデータ | ![]() | 62.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 18.2 KB 18.2 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 10.7 KB | 表示 | ![]() |
画像 | ![]() | 52.6 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7pfdMC ![]() 7petC ![]() 7peuC ![]() 7pevC ![]() 7pewC ![]() 7pexC ![]() 7peyC ![]() 7pezC ![]() 7pf0C ![]() 7pf2C ![]() 7pf3C ![]() 7pf4C ![]() 7pf5C ![]() 7pf6C ![]() 7pfaC ![]() 7pfcC ![]() 7pfeC ![]() 7pffC ![]() 7pftC ![]() 7pfuC ![]() 7pfvC ![]() 7pfwC ![]() 7pfxC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
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試料の構成要素
+全体 : Nucleosome 1 from 4x197 nucleosome array
+超分子 #1: Nucleosome 1 from 4x197 nucleosome array
+超分子 #2: Histones
+超分子 #3: DNA
+分子 #1: Histone H3.2
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2B type 1-K
+分子 #7: Histone H1.4
+分子 #5: DNA (172-MER)
+分子 #6: DNA (172-MER)
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.1 mg/mL |
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緩衝液 | pH: 7 |
凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |