+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3954 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of the human INO80 complex bound to nucleosome | ||||||||||||
マップデータ | map of human INO80 bound to nucleosome | ||||||||||||
試料 |
| ||||||||||||
機能・相同性 | 機能・相同性情報 positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / dynein axonemal particle / R2TP complex / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body ...positive regulation of nuclear cell cycle DNA replication / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / dynein axonemal particle / R2TP complex / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / positive regulation of telomerase RNA localization to Cajal body / regulation of double-strand break repair / Ino80 complex / UV-damage excision repair / protein folding chaperone complex / ATP-dependent chromatin remodeler activity / box C/D snoRNP assembly / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / mitotic sister chromatid segregation / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / negative regulation of tumor necrosis factor-mediated signaling pathway / alpha-tubulin binding / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / spindle assembly / ATP-dependent activity, acting on DNA / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / regulation of DNA repair / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / TBP-class protein binding / telomere organization / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / telomere maintenance / positive regulation of DNA repair / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / DNA helicase activity / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / cellular response to estradiol stimulus / HDACs deacetylate histones / cellular response to ionizing radiation / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / DNA Damage Recognition in GG-NER / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / chromatin DNA binding / ADP binding / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / spindle / nuclear matrix / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / synthetic construct (人工物) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.8 Å | ||||||||||||
データ登録者 | Ayala R / Willhoft O / Aramayo RJ / Wilkinson M / McCormack EA / Ocloo L / Wigley DB / Zhang X | ||||||||||||
資金援助 | 英国, 3件
| ||||||||||||
引用 | ジャーナル: Nature / 年: 2018 タイトル: Structure and regulation of the human INO80-nucleosome complex. 著者: Rafael Ayala / Oliver Willhoft / Ricardo J Aramayo / Martin Wilkinson / Elizabeth A McCormack / Lorraine Ocloo / Dale B Wigley / Xiaodong Zhang / 要旨: Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. ...Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines . Biochemical studies have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding , histone exchange and nucleosome spacing remain poorly understood. Although some remodellers work as monomers , others work as highly cooperative dimers. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5-IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain-unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains. | ||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_3954.map.gz | 10.5 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-3954-v30.xml emd-3954.xml | 31 KB 31 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_3954_fsc.xml | 9.7 KB | 表示 | FSCデータファイル |
画像 | emd_3954.png | 65.5 KB | ||
その他 | emd_3954_additional.map.gz | 63.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3954 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3954 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3954_validation.pdf.gz | 258.2 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_3954_full_validation.pdf.gz | 257.3 KB | 表示 | |
XML形式データ | emd_3954_validation.xml.gz | 11.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3954 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3954 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_3954.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | map of human INO80 bound to nucleosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: blurred map (with a factor applied of 250)...
ファイル | emd_3954_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | blurred map (with a factor applied of 250) to help visualise the nucleosome and flexible regions of the complex that have not been modelled | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Complex of core human INO80 with nucleosome
+超分子 #1: Complex of core human INO80 with nucleosome
+超分子 #2: nucleosome
+超分子 #4: human INO80
+超分子 #3: Histone subunits
+分子 #1: RuvB-like 1
+分子 #2: RuvB-like 2
+分子 #3: DNA helicase INO80
+分子 #4: Actin-related protein 5
+分子 #5: Histone H3.1
+分子 #6: Histone H4
+分子 #7: Histone H2A type 1-B/E
+分子 #8: Histone H2B type 1-J
+分子 #9: INO80 complex subunit B
+分子 #10: DNA (142-MER)
+分子 #11: DNA (142-MER)
+分子 #12: ADENOSINE-5'-DIPHOSPHATE
+分子 #13: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 8 |
---|---|
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 80.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |