+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ooc | |||||||||||||||
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タイトル | CryoEM Structure INO80core Hexasome complex Rvb core refinement state1 | |||||||||||||||
要素 |
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キーワード | DNA BINDING PROTEIN (DNA結合タンパク質) / ATP-dependent chromatin remodeler | |||||||||||||||
機能・相同性 | 機能・相同性情報 DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / ATP-dependent activity, acting on DNA / helicase activity / 紡錘体 / 動原体 ...DASH complex / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / attachment of spindle microtubules to kinetochore / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / ATP-dependent activity, acting on DNA / helicase activity / 紡錘体 / 動原体 / chromatin organization / ヘリカーゼ / クロマチンリモデリング / DNA修復 / ATP hydrolysis activity / ATP binding / 細胞核 類似検索 - 分子機能 | |||||||||||||||
生物種 | Thermochaetoides thermophila (菌類) | |||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.93 Å | |||||||||||||||
データ登録者 | Zhang, M. / Jungblut, A. / Hoffmann, T. / Eustermann, S. | |||||||||||||||
資金援助 | ドイツ, European Union, 4件
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引用 | ジャーナル: Science / 年: 2023 タイトル: Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling. 著者: Min Zhang / Anna Jungblut / Franziska Kunert / Luis Hauptmann / Thomas Hoffmann / Olga Kolesnikova / Felix Metzner / Manuela Moldt / Felix Weis / Frank DiMaio / Karl-Peter Hopfner / Sebastian Eustermann / 要旨: Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In ...Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation. #1: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2018 タイトル: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. 著者: Tristan Ian Croll / 要旨: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model. #2: ジャーナル: Biochem J / 年: 2021 タイトル: New tools for automated cryo-EM single-particle analysis in RELION-4.0. 著者: Dari Kimanius / Liyi Dong / Grigory Sharov / Takanori Nakane / Sjors H W Scheres / 要旨: We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient ...We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient descent algorithm with adaptive moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on 12 publicly available cryo-EM data sets. #3: ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2010 タイトル: Features and development of Coot. 著者: P Emsley / B Lohkamp / W G Scott / K Cowtan / 要旨: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed. | |||||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8ooc.cif.gz | 731.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ooc.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8ooc.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/oo/8ooc ftp://data.pdbj.org/pub/pdb/validation_reports/oo/8ooc | HTTPS FTP |
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-関連構造データ
関連構造データ | 17010MC 8oo7C 8oo9C 8ooaC 8oofC 8ookC 8oopC 8oorC 8oosC 8ootC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
-タンパク質 , 6種, 10分子 ABCDEFGHIJ
#1: タンパク質 | 分子量: 50451.848 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) Thermochaetoides thermophila (菌類) 遺伝子: CTHT_0006820 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G0RYI5, ヘリカーゼ #2: タンパク質 | 分子量: 53212.746 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) Thermochaetoides thermophila (菌類) 遺伝子: CTHT_0006170 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G0RYC2, ヘリカーゼ #3: タンパク質 | | 分子量: 130887.656 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Thermochaetoides thermophila (菌類) 発現宿主: Trichoplusia ni (イラクサキンウワバ) 参照: 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 #4: タンパク質 | | 分子量: 53345.980 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Thermochaetoides thermophila (菌類) 遺伝子: CTHT_0004910 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G0RY01 #5: タンパク質 | | 分子量: 23127.523 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIV IDNGSHSVRAGWNFEDKPRLAIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFE AGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTEAVANLPYSRKSMSEIIFECY ...詳細: MAPSAVAEPPPIPQRDEPWKRLPPPTVYPVKEARFEKYIPPQLDGRERALAQPPGQVAIV IDNGSHSVRAGWNFEDKPRLAIPPIMSKYRDRKMGKTFSFAGSDCYADTTARSHIRNAFE AGTGIVSNWDVMEHVLDYVFVKLGMNECDGAIDMPIVMTEAVANLPYSRKSMSEIIFECY GAPSLVYGIDSLFSFRHNQGQTGLVVSSSYSATHVIPVYNRKALLSQAIRLNWGGWHMAE YMLKLLKLKYYTGFPGKLNSSQTEHMVRDFCYVSLDYDRELAGYLDWTGLEDRERIVQYP YTEEVVVQKTEEELARIAERKKESGRRLQEQAAKMRLERLMKKEQELEYYKDIQRRMQGE SKKEIKRLLDEAELKDEAALERVIRDLERSIKRARQKDLGEPEEEEVPDFSLLDVPDDQL DEAGLRQKRQQRLLKSNWEARQRAKAEKEAEKARLAEEARLDEERRKNDLEGWLEEKRQL RLAKLNQLKERERLKADLGNRKSLASQIRMKNIANLASDNPTGSGSRKRRRGGAGADQDD DFGADDADWGVYRSVAIGANKGDDSDDEEGEEDLEAAIRSLENDLLRYDKTFSYDMTLDA QRDWSKSLLHAFRYGPRPFDPSSQAETHRVHLNVERIRVPEVLFQPAAIAGVDQAGLVEI AGDILCQRLPSLPGIQDAPDAFLRDVFLTGGNTLFQNFDERLRQGLMALLPVGAPLRVRR AQDAILDAWRGAAGWACTEEAKAAWITREEYLEKGGEYIKEHDLGNAFA 由来: (組換発現) Thermochaetoides thermophila (菌類) 遺伝子: CTHT_0032670 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G0S590 #6: タンパク質 | | 分子量: 87773.086 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Thermochaetoides thermophila (菌類) 遺伝子: CTHT_0032660 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G0S589 |
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-非ポリマー , 3種, 8分子
#7: 化合物 | ChemComp-ADP / #8: 化合物 | ChemComp-MG / | #9: 化合物 | ChemComp-ATP / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: INO80 core module in complex with hexasome / タイプ: COMPLEX 詳細: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct ...詳細: 11-subunit ct INO80 contains two modules (core and Arp8 module) Each module was picked and analyzed separately The core module + hexasome has an overall weight of 0.861MDa The 11-subunit ct INO80 + hexasome has an overall weight of 1.1MDa Ino80, Ies2, Ies6, Ies4,Arp6, Rvb1, Rvb2, Arp8, Arp4, Actin, Taf14 Hexasome DNA, 2xH3, 2xH4, H2A, H2B Entity ID: #1-#6 / 由来: RECOMBINANT |
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分子量 | 値: 0.861 MDa / 実験値: NO |
由来(天然) | 生物種: Thermochaetoides thermophila (菌類) |
由来(組換発現) | 生物種: Trichoplusia ni (イラクサキンウワバ) |
緩衝液 | pH: 7.5 詳細: 30mM HEPES, pH7.5 50mM NaCl 0.25mM CaCl2 0.25mM DTT 2mM ADP 3.3mM MgCl2 10mM NaF 2mM AlCl3 0.05% octyl-beta-glucoside |
試料 | 濃度: 0.88 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: 11-subunit ctINO80 reconstituted with hexasome |
試料支持 | 詳細: 10% Oxygene 90% Argon / グリッドの材料: COPPER / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/1 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 281 K 詳細: wait time of 5s, blot force at 3, and a blot time of 2s with Whatman blotting paper (Cytiva, CAT No. 10311807) |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 800 nm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 50.36 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 15384 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 2137460 詳細: Particles were initially picked by WARP to generate an initial model, which was subsequently used for the 3D template picking | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.93 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 72400 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER | ||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 8AV6 Accession code: 8AV6 / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 86.68 Å2 | ||||||||||||||||||||||||||||||||
拘束条件 |
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