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基本情報
登録情報 | データベース: EMDB / ID: EMD-20507 | |||||||||
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タイトル | Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome | |||||||||
![]() | Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome | |||||||||
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![]() | nucleosome / DNA-binding protein / ATP-dependent chromatin remodeler / ISWI / STRUCTURAL PROTEIN-DNA complex | |||||||||
機能・相同性 | ![]() chromatin remodeling => GO:0006338 / ATP-dependent chromatin remodeler activity => GO:0140658 / HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs ...chromatin remodeling => GO:0006338 / ATP-dependent chromatin remodeler activity => GO:0140658 / HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / polytene chromosome / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / nuclear chromosome / heterochromatin organization / nucleosome binding / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / nucleic acid binding / protein heterodimerization activity / chromatin / protein-containing complex binding / DNA binding / ATP binding / nucleus 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: 4.07 Å | |||||||||
![]() | Chittori S / Subramaniam S | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome. 著者: Sagar Chittori / Jingjun Hong / Yawen Bai / Sriram Subramaniam / ![]() ![]() 要旨: ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report ...ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3. Density for other regions of ISWI is not observed, presumably due to disorder. Comparison with the structure of the free nucleosome reveals that although the histone core remains largely unchanged, remodeler binding causes perturbations in the nucleosomal DNA resulting in a bulge near the SHL2 site. Overall, the structure of the nucleotide-free ISWI-nucleosome complex is similar to the corresponding regions of the recently reported ADP bound ISWI-nucleosome structures, which are significantly different from that observed for the ADP-BeFx bound structure. Our findings are relevant to the initial step of ISWI binding to the nucleosome and provide additional insights into the nucleosome remodeling process driven by ISWI. | |||||||||
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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注釈 | Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
+全体 : Complex of the ATPase domain of ISWI bound to the nucleosome
+超分子 #1: Complex of the ATPase domain of ISWI bound to the nucleosome
+超分子 #2: nucleosome
+超分子 #3: ATPase domain of ISWI
+分子 #1: Histone H3
+分子 #2: Histone H4
+分子 #3: Histone H2A
+分子 #4: Histone H2B
+分子 #7: chromatin remodeling factor ISWI
+分子 #5: DNA (147-MER)
+分子 #6: DNA (147-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
緩衝液 | pH: 7.4 |
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グリッド | 詳細: unspecified |
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 K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 39.0 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 |
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画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: 詳細: Histones: 4X23 DNA: 6BUZ ISWI: 5JXR |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.07 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 32529 |
初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: OTHER |