+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19499 | ||||||||||||
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タイトル | Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom | ||||||||||||
マップデータ | Sharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
試料 |
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キーワード | actin / formin / Cdc12 / profilin / 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 / MGMT-mediated DNA damage reversal / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / MGMT-mediated DNA damage reversal / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / regulation of transepithelial transport / DNA-methyltransferase activity / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / postsynaptic actin cytoskeleton / brahma complex / Tat protein binding / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / regulation of G0 to G1 transition / Signaling by ROBO receptors / regulation of actin filament polymerization / Formation of annular gap junctions / dense body / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / DNA ligation / apical protein localization / mating projection tip / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / adherens junction assembly / barbed-end actin filament capping / Prefoldin mediated transfer of substrate to CCT/TriC / DNA alkylation repair / RHOF GTPase cycle / positive regulation of ATP-dependent activity / Adherens junctions interactions / proline-rich region binding / tight junction / PCP/CE pathway / positive regulation of ruffle assembly / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of norepinephrine uptake / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / negative regulation of stress fiber assembly / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of actin filament polymerization / cortical cytoskeleton / maintenance of blood-brain barrier / cell division site / positive regulation of stem cell population maintenance / positive regulation of epithelial cell migration / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / kinesin binding / actin filament bundle assembly / calyx of Held / negative regulation of cell differentiation / actin monomer binding / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / EPHB-mediated forward signaling / actin filament polymerization / phosphotyrosine residue binding / axonogenesis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / platelet aggregation 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: 6.25 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_19499.map.gz | 398.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19499-v30.xml emd-19499.xml | 30.9 KB 30.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19499_fsc.xml | 18.1 KB | 表示 | FSCデータファイル |
画像 | emd_19499.png | 90.2 KB | ||
マスクデータ | emd_19499_msk_1.map | 421.9 MB | マスクマップ | |
Filedesc metadata | emd-19499.cif.gz | 8.7 KB | ||
その他 | emd_19499_additional_1.map.gz emd_19499_half_map_1.map.gz emd_19499_half_map_2.map.gz | 206.5 MB 392 MB 392 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19499 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19499 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19499_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19499_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_19499_validation.xml.gz | 25.3 KB | 表示 | |
CIF形式データ | emd_19499_validation.cif.gz | 33.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19499 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19499 | 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_19499.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
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_19499_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 F-actin...
ファイル | emd_19499_additional_1.map | ||||||||||||
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注釈 | 3D-refined, unsharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
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 F-actin barbed...
ファイル | emd_19499_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half map 2 of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
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 F-actin barbed...
ファイル | emd_19499_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half map 1 of the F-actin barbed end bound by Cdc12 and profilin-S71M | ||||||||||||
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 : Actin-formin-profilin ring complex: the phalloidin-stabilized F-a...
+超分子 #1: Actin-formin-profilin ring complex: the phalloidin-stabilized F-a...
+超分子 #2: Actin filament
+超分子 #3: Dimeric FH1FH2 domain of S. Pombe Cdc12
+超分子 #4: Profilin-1-S29C/S71M
+超分子 #5: Phalloidin
+分子 #1: Actin, cytoplasmic 1, N-terminally processed
+分子 #2: Methylated-DNA--protein-cysteine methyltransferase,Cell division ...
+分子 #3: Phalloidin (Amanita phalloides)
+分子 #4: Profilin-1
+分子 #5: ADENOSINE-5'-DIPHOSPHATE
+分子 #6: MAGNESIUM ION
+分子 #7: 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: 5287 / 平均電子線量: 63.3 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): 3.0 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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詳細 | Refinement performed using phenix real-space refine | |||||||||
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | |||||||||
得られたモデル | PDB-8rty: |