+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8oot | |||||||||||||||
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タイトル | CryoEM Structure INO80core Hexasome complex Arp5 Ies6 refinement state2 | |||||||||||||||
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 / 紡錘体 / 動原体 / クロマチンリモデリング / regulation of DNA-templated transcription / 細胞質 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: 2.85 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: Real-space refinement in PHENIX for cryo-EM and crystallography. 著者: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / 要旨: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. #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 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. #4: 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 | 8oot.cif.gz | 131.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8oot.ent.gz | 97.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8oot.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/8oot ftp://data.pdbj.org/pub/pdb/validation_reports/oo/8oot | HTTPS FTP |
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-関連構造データ
関連構造データ | 17028MC 8oo7C 8oo9C 8ooaC 8oocC 8oofC 8ookC 8oopC 8oorC 8oosC 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
#1: タンパク質 | 分子量: 23127.523 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_0032670 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G0S590 |
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#2: 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 |
#3: 化合物 | ChemComp-ATP / |
#4: 化合物 | ChemComp-MG / |
研究の焦点であるリガンドがあるか | Y |
-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 |
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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 | 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: 2.85 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 98967 / 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: 6FML Accession code: 6FML / 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: 81.33 Å2 | ||||||||||||||||||||||||||||||||
拘束条件 |
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