+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20770 | ||||||||||||
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タイトル | CryoEM structure of human Arp2/3 complex with bound NPFs | ||||||||||||
マップデータ | Cryo-EM structure of human Arp2/3 complex bound to two nucleation promoting factors (B-factor sharpened). | ||||||||||||
試料 |
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キーワード | actin / ATPase / actin related protein / arp / cytoskeleton / Arp2-3 complex / actin nucleation / actin branching / CONTRACTILE PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / muscle cell projection membrane / negative regulation of membrane tubulation / meiotic cytokinesis / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis ...tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / muscle cell projection membrane / negative regulation of membrane tubulation / meiotic cytokinesis / spindle localization / membrane invagination / positive regulation of clathrin-dependent endocytosis / actin polymerization-dependent cell motility / plasma membrane tubulation / Arp2/3 protein complex / asymmetric cell division / negative regulation of lymphocyte migration / Arp2/3 complex-mediated actin nucleation / postsynapse organization / actin nucleation / regulation of cell projection assembly / actin cap / vesicle organization / postsynaptic actin cytoskeleton organization / vesicle transport along actin filament / regulation of actin filament polymerization / vesicle budding from membrane / positive regulation of chemotaxis / protein-containing complex localization / dendritic spine morphogenesis / positive regulation of filopodium assembly / regulation of postsynapse organization / establishment or maintenance of cell polarity / positive regulation of actin filament polymerization / cell leading edge / filamentous actin / brush border / positive regulation of double-strand break repair via homologous recombination / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / EPHB-mediated forward signaling / cytoskeletal protein binding / actin filament polymerization / cellular response to nerve growth factor stimulus / cell projection / FCGR3A-mediated phagocytosis / response to bacterium / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / response to estrogen / regulation of protein localization / azurophil granule lumen / cell-cell junction / Clathrin-mediated endocytosis / actin cytoskeleton / cell migration / lamellipodium / response to estradiol / site of double-strand break / actin binding / cell cortex / actin cytoskeleton organization / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / postsynapse / endosome / neuron projection / cell division / Golgi membrane / focal adhesion / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / enzyme binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾) / Homo sapiens (ヒト) / Mus musculus (ハツカネズミ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | ||||||||||||
データ登録者 | Zimmet A / van Eeuwen T | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Sci Adv / 年: 2020 タイトル: Cryo-EM structure of NPF-bound human Arp2/3 complex and activation mechanism. 著者: Austin Zimmet / Trevor Van Eeuwen / Malgorzata Boczkowska / Grzegorz Rebowski / Kenji Murakami / Roberto Dominguez / 要旨: Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation- ...Actin-related protein (Arp) 2/3 complex nucleates branched actin networks that drive cell motility. It consists of seven proteins, including two actin-related subunits (Arp2 and Arp3). Two nucleation-promoting factors (NPFs) bind Arp2/3 complex during activation, but the order, specific interactions, and contribution of each NPF to activation are unresolved. Here, we report the cryo-electron microscopy structure of recombinantly expressed human Arp2/3 complex with two WASP family NPFs bound and address the mechanism of activation. A cross-linking assay that captures the transition of the Arps into the activated filament-like conformation shows that actin binding to NPFs favors this transition. Actin-NPF binding to Arp2 precedes binding to Arp3 and is sufficient to promote the filament-like conformation but not activation. Structure-guided mutagenesis of the NPF-binding sites reveals their distinct roles in activation and shows that, contrary to budding yeast Arp2/3 complex, NPF-mediated delivery of actin at the barbed end of both Arps is required for activation of human Arp2/3 complex. | ||||||||||||
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_20770.map.gz | 117.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20770-v30.xml emd-20770.xml | 28.7 KB 28.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_20770_fsc.xml | 11.5 KB | 表示 | FSCデータファイル |
画像 | emd_20770.png | 41.8 KB | ||
Filedesc metadata | emd-20770.cif.gz | 8.6 KB | ||
その他 | emd_20770_additional.map.gz | 62.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20770 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20770 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_20770_validation.pdf.gz | 525.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_20770_full_validation.pdf.gz | 525.1 KB | 表示 | |
XML形式データ | emd_20770_validation.xml.gz | 12.4 KB | 表示 | |
CIF形式データ | emd_20770_validation.cif.gz | 16.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20770 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20770 | 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_20770.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of human Arp2/3 complex bound to two nucleation promoting factors (B-factor sharpened). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.836 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
-追加マップ: Cryo-EM structure of human Arp2/3 complex bound to...
ファイル | emd_20770_additional.map | ||||||||||||
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注釈 | Cryo-EM structure of human Arp2/3 complex bound to two nucleation promoting factors | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Cryo-EM structure of human Arp2/3 complex with bound NPFs
+超分子 #1: Cryo-EM structure of human Arp2/3 complex with bound NPFs
+分子 #1: Actin-related protein 3
+分子 #2: Actin-related protein 2
+分子 #3: Actin-related protein 2/3 complex subunit 1B
+分子 #4: Actin-related protein 2/3 complex subunit 2
+分子 #5: Actin-related protein 2/3 complex subunit 3
+分子 #6: Actin-related protein 2/3 complex subunit 4
+分子 #7: Actin-related protein 2/3 complex subunit 5
+分子 #8: Neural Wiskott-Aldrich syndrome protein
+分子 #9: MAGNESIUM ION
+分子 #10: ADENOSINE-5'-TRIPHOSPHATE
-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 | 5 mg/mL | |||||||||||||||||||||
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緩衝液 | pH: 7 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 200 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: AIR 詳細: Grids glow discharged with easiGLOW glow discharger at 0.3 mBar, 25mA for 1 minute | |||||||||||||||||||||
凍結 | 凍結剤: ETHANE / 装置: LEICA EM CPC 詳細: Grids manually blotted for 3 seconds with Whatman 41 filter paper and manually plunged on Leica EM CPC manual plunger.. | |||||||||||||||||||||
詳細 | This sample was monodisperse |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
詳細 | Data collected in super resolution mode. Illuminated area of 1.01um. Nominal Dose of 40a/A^2 and a dose rate of 4.87 e-/s/pixel. 2 or 5 exposures per hole by image shift. |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 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: 2 / 実像数: 5004 / 平均露光時間: 7.0 sec. / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): -3.5 µm / 最小 デフォーカス(公称値): -1.5 µm / 倍率(公称値): 165000 |
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 |