+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4280 | |||||||||
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タイトル | CryoEM structure of INO80core Nucleosome complex in open grappler conformation | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RMTs methylate histone arginines / heterochromatin formation => GO:0031507 / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / Metalloprotease DUBs / UCH proteinases / Ub-specific processing proteases / attachment of spindle microtubules to kinetochore / R2TP complex ...RMTs methylate histone arginines / heterochromatin formation => GO:0031507 / DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / Metalloprotease DUBs / UCH proteinases / Ub-specific processing proteases / attachment of spindle microtubules to kinetochore / R2TP complex / chromatin => GO:0000785 / Swr1 complex / attachment of mitotic spindle microtubules to kinetochore / Ino80 complex / box C/D snoRNP assembly / NuA4 histone acetyltransferase complex / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / 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 / DNA helicase activity / 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 / heterochromatin formation / RMTs methylate histone arginines / mitotic spindle / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / kinetochore / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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 / 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 / DNA helicase / Estrogen-dependent gene expression / chromatin remodeling / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / DNA repair / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / DNA binding / extracellular space / extracellular exosome 類似検索 - 分子機能 | |||||||||
生物種 | Chaetomium thermophilum var. thermophilum DSM 1495 (菌類) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.62 Å | |||||||||
データ登録者 | Eustermann S / Schall K / Strauss M / Hopfner KP | |||||||||
引用 | ジャーナル: Nature / 年: 2018 タイトル: Structural basis for ATP-dependent chromatin remodelling by the INO80 complex. 著者: Sebastian Eustermann / Kevin Schall / Dirk Kostrewa / Kristina Lakomek / Mike Strauss / Manuela Moldt / Karl-Peter Hopfner / 要旨: In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone ...In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers such as the 15-subunit INO80 complex . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA. The structures and mechanisms of these remodelling reactions are currently unknown. Here we report the cryo-electron microscopy structure of the evolutionarily conserved core of the INO80 complex from the fungus Chaetomium thermophilum bound to a nucleosome, at a global resolution of 4.3 Å and with major parts at 3.7 Å. The INO80 core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. An Rvb1/Rvb2 AAA ATPase heterohexamer is an assembly scaffold for the complex and acts as a 'stator' for the motor and nucleosome-gripping subunits. The Swi2/Snf2 ATPase motor binds to nucleosomal DNA at superhelical location -6, unwraps approximately 15 base pairs, disrupts the H2A-DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind superhelical locations -2 and -3 to act as a counter grip for the motor, on the other side of the H2A-H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 actin-fold and entry DNA over a distance of about 90 Å and packs against histone H2A-H2B near the 'acidic patch'. Our structure together with biochemical data suggests a unified mechanism for nucleosome sliding and histone editing by INO80. The motor is part of a macromolecular ratchet, persistently pumping entry DNA across the H2A-H2B dimer against the Arp5 grip until a large nucleosome translocation step occurs. The transient exposure of H2A-H2B by motor activity as well as differential recognition of H2A.Z and H2A may regulate histone exchange. | |||||||||
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_4280.map.gz | 87.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4280-v30.xml emd-4280.xml | 13.9 KB 13.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4280_fsc.xml | 12.2 KB | 表示 | FSCデータファイル |
画像 | emd_4280.png | 53.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4280 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4280 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4280_validation.pdf.gz | 251.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4280_full_validation.pdf.gz | 250.9 KB | 表示 | |
XML形式データ | emd_4280_validation.xml.gz | 12.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4280 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4280 | 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_4280.map.gz / 形式: CCP4 / 大きさ: 149.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.06 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 : INO80core Nucleosome complex
全体 | 名称: INO80core Nucleosome complex |
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要素 |
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-超分子 #1: INO80core Nucleosome complex
超分子 | 名称: INO80core Nucleosome complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#15 |
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由来(天然) | 生物種: Chaetomium thermophilum var. thermophilum DSM 1495 (菌類) |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
分子量 | 理論値: 1 MDa |
-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 | particle |
-試料調製
濃度 | 1 mg/mL |
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緩衝液 | pH: 8 詳細: 20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside |
グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 281 K / 装置: LEICA EM GP |
詳細 | Monodisperse sample: INO80core complex reconstituted with nucleosomal substrate was purified by gelfiltration. Addition of nucleotides or crosslinking was not required |
-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: COUNTING / デジタル化 - 画像ごとのフレーム数: 1-40 / 撮影したグリッド数: 1 / 実像数: 3992 / 平均電子線量: 59.6 e/Å2 詳細: Images were collected in movie mode with 4 frames per second and 10s total aquisition |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 最小 デフォーカス(補正後): 1.3 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.5 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |