+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2857 | |||||||||
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タイトル | CryoEM reconstruction of dynactin complex from pig brain at 4.0 Angstrom resolution overall | |||||||||
マップデータ | CryoEM reconstruction of the Arp filament of dynactin complex from at 3.5 angstrom resolution | |||||||||
試料 |
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キーワード | dynactin (ダイナクチン) / dynein co-factor / actin-like filament / cellular cargo transport | |||||||||
機能・相同性 | 機能・相同性情報 retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / COPI-independent Golgi-to-ER retrograde traffic ...retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / COPI-independent Golgi-to-ER retrograde traffic / ダイナクチン / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Clathrin-mediated endocytosis / F-actin capping protein complex / negative regulation of filopodium assembly / cellular response to cytochalasin B / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / barbed-end actin filament capping / coronary vasculature development / adherens junction assembly / regulation of lamellipodium assembly / 密着結合 / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / regulation of norepinephrine uptake / aorta development / COPI-mediated anterograde transport / regulation of synaptic vesicle endocytosis / ventricular septum development / NuA4 histone acetyltransferase complex / apical junction complex / establishment or maintenance of cell polarity / dynein complex binding / cortical cytoskeleton / nitric-oxide synthase binding / kinesin binding / ヘルト萼状シナプス / 刷子縁 / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / axon cytoplasm / 軸索誘導 / mitotic spindle organization / 運動性 / マイクロフィラメント / 接着結合 / 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 / Schaffer collateral - CA1 synapse / cell morphogenesis / 動原体 / cytoplasmic ribonucleoprotein granule / ヌクレオソーム / actin filament binding / マイクロフィラメント / lamellipodium / 細胞皮質 / actin cytoskeleton organization / 核膜 / 細胞骨格 / hydrolase activity / regulation of cell cycle / ribonucleoprotein complex / 神経繊維 / focal adhesion / 中心体 / glutamatergic synapse / シナプス / protein kinase binding / protein-containing complex / 核質 / ATP binding / 生体膜 / identical protein binding / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Sus scrofa domesticus (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
データ登録者 | Zhang K / Urnavicius L / Diamant AG / Motz C / Schlager MA / Yu M / Patel NA / Robinson CV / Carter AP | |||||||||
引用 | ジャーナル: Science / 年: 2015 タイトル: The structure of the dynactin complex and its interaction with dynein. 著者: Linas Urnavicius / Kai Zhang / Aristides G Diamant / Carina Motz / Max A Schlager / Minmin Yu / Nisha A Patel / Carol V Robinson / Andrew P Carter / 要旨: Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our ...Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our reconstruction reveals how dynactin is built around a filament containing eight copies of the actin-related protein Arp1 and one of β-actin. The filament is capped at each end by distinct protein complexes, and its length is defined by elongated peptides that emerge from the α-helical shoulder domain. A further 8.2 angstrom structure of the complex between dynein, dynactin, and the motility-inducing cargo adaptor Bicaudal-D2 shows how the translational symmetry of the dynein tail matches that of the dynactin filament. The Bicaudal-D2 coiled coil runs between dynein and dynactin to stabilize the mutually dependent interactions between all three components. | |||||||||
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_2857.map.gz | 1.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2857-v30.xml emd-2857.xml | 18.6 KB 18.6 KB | 表示 表示 | EMDBヘッダ |
画像 | image2857.png | 137.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2857 | 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_2857.map.gz / 形式: CCP4 / 大きさ: 16.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | CryoEM reconstruction of the Arp filament of dynactin complex from at 3.5 angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.34 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 : Dynactin complex from pig brain
+超分子 #1000: Dynactin complex from pig brain
+分子 #1: Actin related protein 1
+分子 #2: Actin related protein 11
+分子 #3: beta-actin
+分子 #4: Dynactin subunit 1
+分子 #5: Dynactin subunit 2
+分子 #6: Dynactin subunit 3
+分子 #7: Actin capping protein
+分子 #8: Dynactin subunit 4
+分子 #9: Dynactin subunit 5
+分子 #10: Dynactin subunit 6
-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 | 0.07 mg/mL |
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緩衝液 | pH: 6.5 詳細: 50mM KCl, 25mM KH2PO4-K2HPO4, 5mM DDT, 1mM MgCl2, 0.1 mM ATP |
グリッド | 詳細: R2/2 400 square mesh copper grid with thin carbon support |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 105 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 102967 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 7.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
温度 | 最低: 80 K / 最高: 100 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 96,000 times nominal magnification Legacy - Electron beam tilt params: 0 |
日付 | 2014年9月12日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 14423 / 平均電子線量: 54 e/Å2 / ビット/ピクセル: 32 |
Tilt angle min | 0 |
Tilt angle max | 0 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: Each particle by Gctf |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Relion 詳細: Final map were sharpened to 3.5 angstrom from a 4.1 angstrom map in overall This map was only used for analysis of Arp filament of dynactin 使用した粒子像数: 115044 |
詳細 | The particles were selected using a GPU accelerated automatic program Gautomatch. The CTF parameter were determined and refined using a GPU accelerated program Gctf. |