+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0777 | |||||||||
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タイトル | The ClassA RSC-Nucleosome Complex | |||||||||
マップデータ | The ClassA RSC-Nucleosome Complex | |||||||||
試料 |
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キーワード | chromatin remodeler / SWI/SNF family / DNA BINDING PROTEIN-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 regulation of sporulation resulting in formation of a cellular spore / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / DNA translocase activity / RSC-type complex ...regulation of sporulation resulting in formation of a cellular spore / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / chromatin remodeling at centromere / regulation of nuclear cell cycle DNA replication / plasmid maintenance / Platelet degranulation / DNA translocase activity / RSC-type complex / UV-damage excision repair / sister chromatid cohesion / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / nuclear chromosome / sporulation resulting in formation of a cellular spore / NuA4 histone acetyltransferase complex / rRNA transcription / chromosome, centromeric region / nucleosome binding / ATP-dependent activity, acting on DNA / meiotic cell cycle / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / cytoskeleton organization / lysine-acetylated histone binding / helicase activity / DNA-templated transcription initiation / chromosome segregation / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / base-excision repair / chromatin DNA binding / G2/M transition of mitotic cell cycle / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / DNA helicase / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / structural molecule activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288c (パン酵母) / Xenopus laevis (アフリカツメガエル) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.13 Å | |||||||||
データ登録者 | Ye YP / Wu H | |||||||||
引用 | ジャーナル: Science / 年: 2019 タイトル: Structure of the RSC complex bound to the nucleosome. 著者: Youpi Ye / Hao Wu / Kangjing Chen / Cedric R Clapier / Naveen Verma / Wenhao Zhang / Haiteng Deng / Bradley R Cairns / Ning Gao / Zhucheng Chen / 要旨: The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into ...The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo-electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into the adenosine triphosphatase motor, the actin-related protein module, and the substrate recruitment module (SRM). RSC binds the nucleosome mainly through the motor, with the auxiliary subunit Sfh1 engaging the H2A-H2B acidic patch to enable nucleosome ejection. SRM is organized into three substrate-binding lobes poised to bind their respective nucleosomal epitopes. The relative orientations of the SRM and the motor on the nucleosome explain the directionality of DNA translocation and promoter nucleosome repositioning by RSC. Our findings shed light on RSC assembly and functionality, and they provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_0777.map.gz | 20.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0777-v30.xml emd-0777.xml | 38.3 KB 38.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0777.png | 72.2 KB | ||
Filedesc metadata | emd-0777.cif.gz | 12.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0777 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_0777.map.gz / 形式: CCP4 / 大きさ: 22.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The ClassA RSC-Nucleosome Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.14 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
-試料の構成要素
+全体 : RSC
+超分子 #1: RSC
+分子 #1: Histone H4
+分子 #2: Histone H3.2
+分子 #3: Histone H2A
+分子 #6: Nuclear protein STH1/NPS1
+分子 #7: Actin-related protein 7
+分子 #8: Regulator of Ty1 transposition protein 102
+分子 #9: Chromatin structure-remodeling complex subunit RSC7
+分子 #10: Chromatin structure-remodeling complex protein RSC8
+分子 #11: Chromatin structure-remodeling complex subunit RSC9
+分子 #12: Chromatin structure-remodeling complex protein RSC6
+分子 #13: Chromatin structure-remodeling complex subunit SFH1
+分子 #14: Chromatin structure-remodeling complex protein RSC58
+分子 #15: High temperature lethal protein 1
+分子 #16: Chromatin structure-remodeling complex protein RSC30
+分子 #17: Chromatin structure-remodeling complex protein RSC3
+分子 #18: Chromatin structure-remodeling complex subunit RSC4
+分子 #19: Chromatin structure-remodeling complex subunit RSC2
+分子 #20: Histone H4
+分子 #21: Actin-like protein ARP9
+分子 #4: DNA 167
+分子 #5: DNA 167
+分子 #22: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | cell |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-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 QUANTUM (4k x 4k) 平均電子線量: 2.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: DARK FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: EMDB MAP |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 7.13 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 45077 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |