+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19496 | ||||||||||||
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タイトル | Structure of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. | ||||||||||||
マップデータ | Sharpened, local-resolution filtered cryo-EM density map of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. | ||||||||||||
試料 |
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キーワード | actin / formin / Cdc12 / actin assembly. / STRUCTURAL PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / medial cortex / mitotic actomyosin contractile ring assembly / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / mitotic actomyosin contractile ring ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / medial cortex / mitotic actomyosin contractile ring assembly / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / mitotic actomyosin contractile ring / morphogenesis of a polarized epithelium / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / protein localization to adherens junction / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / GBAF complex / dense body / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / mating projection tip / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / barbed-end actin filament capping / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / cell division site / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / actin filament bundle assembly / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / axonogenesis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / 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 / DNA Damage Recognition in GG-NER / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / platelet aggregation / VEGFA-VEGFR2 Pathway / nuclear matrix / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Schizosaccharomyces pombe (分裂酵母) / Amanita phalloides (タマゴテングタケ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.56 Å | ||||||||||||
データ登録者 | Oosterheert W / Boiero Sanders M / Funk J / Prumbaum D / Raunser S / Bieling P | ||||||||||||
資金援助 | ドイツ, European Union, 3件
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引用 | ジャーナル: Science / 年: 2024 タイトル: Molecular mechanism of actin filament elongation by formins. 著者: Wout Oosterheert / Micaela Boiero Sanders / Johanna Funk / Daniel Prumbaum / Stefan Raunser / Peter Bieling / 要旨: Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action ...Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation. | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_19496.map.gz | 77.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19496-v30.xml emd-19496.xml | 39.3 KB 39.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19496_fsc.xml | 11.4 KB | 表示 | FSCデータファイル |
画像 | emd_19496.png | 90.3 KB | ||
マスクデータ | emd_19496_msk_1.map | 125 MB | マスクマップ | |
Filedesc metadata | emd-19496.cif.gz | 8.5 KB | ||
その他 | emd_19496_additional_1.map.gz emd_19496_additional_2.map.gz emd_19496_additional_3.map.gz emd_19496_additional_4.map.gz emd_19496_additional_5.map.gz emd_19496_additional_6.map.gz emd_19496_half_map_1.map.gz emd_19496_half_map_2.map.gz | 98.3 MB 97.4 MB 75.9 MB 98.4 MB 98.4 MB 77.2 MB 98.5 MB 98.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19496 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19496 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19496_validation.pdf.gz | 940.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19496_full_validation.pdf.gz | 939.7 KB | 表示 | |
XML形式データ | emd_19496_validation.xml.gz | 18.7 KB | 表示 | |
CIF形式データ | emd_19496_validation.cif.gz | 24.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19496 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19496 | 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_19496.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 | Sharpened, local-resolution filtered cryo-EM density map of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.88 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_19496_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 3D-refined, unsharpened cryo-EM density map of the formin...
ファイル | emd_19496_additional_1.map | ||||||||||||
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注釈 | 3D-refined, unsharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unsharpened cryo-EM density map of actin-Cdc12. This reconstruction...
ファイル | emd_19496_additional_2.map | ||||||||||||
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注釈 | Unsharpened cryo-EM density map of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Composite map of two reconstructions of the formin...
ファイル | emd_19496_additional_3.map | ||||||||||||
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注釈 | Composite map of two reconstructions of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. This map was created using phenix and was used for visualization purposes. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unfiltered half map 1 of actin-Cdc12. This reconstruction...
ファイル | emd_19496_additional_4.map | ||||||||||||
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注釈 | Unfiltered half map 1 of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unfiltered half map 2 of actin-Cdc12. This reconstruction...
ファイル | emd_19496_additional_5.map | ||||||||||||
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注釈 | Unfiltered half map 2 of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Sharpened density map of actin-Cdc12. This reconstruction was...
ファイル | emd_19496_additional_6.map | ||||||||||||
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注釈 | Sharpened density map of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 1 of the formin Cdc12...
ファイル | emd_19496_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half map 1 of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 2 of the formin Cdc12...
ファイル | emd_19496_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half map 2 of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. | ||||||||||||
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 : Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the ...
+超分子 #1: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the ...
+超分子 #2: Actin filament
+超分子 #3: Dimeric FH2 domain of S. Pombe Cdc12
+超分子 #4: Phalloidin.
+分子 #1: Actin, cytoplasmic 1, N-terminally processed
+分子 #2: Cell division control protein 12
+分子 #3: Phalloidin
+分子 #4: ADENOSINE-5'-DIPHOSPHATE
+分子 #5: MAGNESIUM ION
+分子 #6: PHOSPHATE ION
-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
緩衝液 | pH: 7.1 構成要素:
詳細: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP) | ||||||||||||||||||
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グリッド | モデル: Quantifoil R2/1 / 材質: GOLD / 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 - 時間: 90 sec. | ||||||||||||||||||
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 100 % / チャンバー内温度: 286 K / 装置: FEI VITROBOT MARK IV / 詳細: 3 seconds, force 0.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 球面収差補正装置: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 15 eV / 詳細: Gatan energy filter. |
詳細 | 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector. |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 20393 / 平均電子線量: 64.6 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: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.01 mm / 最大 デフォーカス(公称値): 2.7 µm / 最小 デフォーカス(公称値): 1.2 µm / 倍率(公称値): 81000 |
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 |
+画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT | ||||||||||||
得られたモデル | PDB-8rtt: |