+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6447 | |||||||||
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タイトル | Cryo-EM reconstruction of the metavinculin-actin interface | |||||||||
マップデータ | Reconstruction of metavinculin tail domain bound to F-actin | |||||||||
試料 |
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キーワード | actin (アクチン) / metavinculin (ビンキュリン) / vinculin (ビンキュリン) / cell migration (遊走) / adhesion (接着) / mechanosensation / cytoskeleton (細胞骨格) | |||||||||
機能・相同性 | 機能・相同性情報 regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / 接着結合 / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / epithelial cell-cell adhesion / 接着結合 / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / cytoskeletal motor activator activity / regulation of focal adhesion assembly / maintenance of blood-brain barrier / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / 刷子縁 / skeletal muscle myofibril / actin monomer binding / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / cell-matrix adhesion / negative regulation of cell migration / filopodium / cell projection / マイクロフィラメント / morphogenesis of an epithelium / 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 / Signaling by high-kinase activity BRAF mutants / 筋鞘 / MAP2K and MAPK activation / 血小板 / beta-catenin binding / specific granule lumen / calcium-dependent protein binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / extracellular vesicle / Signaling by BRAF and RAF1 fusions / cell-cell junction / Platelet degranulation / lamellipodium / cell body / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / 細胞骨格 / hydrolase activity / 細胞接着 / cadherin binding / 脂質ラフト / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / structural molecule activity / magnesium ion binding / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / 細胞膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Homo sapiens (ヒト) | |||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 8.2 Å | |||||||||
データ登録者 | Kim LY / Thompson PM / Lee HT / Pershad M / Campbell SL / Alushin GM | |||||||||
引用 | ジャーナル: J Mol Biol / 年: 2016 タイトル: The Structural Basis of Actin Organization by Vinculin and Metavinculin. 著者: Laura Y Kim / Peter M Thompson / Hyunna T Lee / Mihir Pershad / Sharon L Campbell / Gregory M Alushin / 要旨: Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. ...Vinculin is an essential adhesion protein that links membrane-bound integrin and cadherin receptors through their intracellular binding partners to filamentous actin, facilitating mechanotransduction. Here we present an 8.5-Å-resolution cryo-electron microscopy reconstruction and pseudo-atomic model of the vinculin tail (Vt) domain bound to F-actin. Upon actin engagement, the N-terminal "strap" and helix 1 are displaced from the Vt helical bundle to mediate actin bundling. We find that an analogous conformational change also occurs in the H1' helix of the tail domain of metavinculin (MVt) upon actin binding, a muscle-specific splice isoform that suppresses actin bundling by Vt. These data support a model in which metavinculin tunes the actin bundling activity of vinculin in a tissue-specific manner, providing a mechanistic framework for understanding metavinculin mutations associated with hereditary cardiomyopathies. | |||||||||
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_6447.map.gz | 25.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6447-v30.xml emd-6447.xml | 13.2 KB 13.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6447.png | 209.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6447 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6447 | 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_6447.map.gz / 形式: CCP4 / 大きさ: 29.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of metavinculin tail domain bound to F-actin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.18 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 : Metavinculin tail domain bound to F-actin
全体 | 名称: Metavinculin tail domain bound to F-actin |
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要素 |
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-超分子 #1000: Metavinculin tail domain bound to F-actin
超分子 | 名称: Metavinculin tail domain bound to F-actin / タイプ: sample / ID: 1000 詳細: Helical filament with one metavinculin tail domain bound per actin protomer 集合状態: One metavinculin tail domain per actin protomer Number unique components: 2 |
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-分子 #1: skeletal muscle actin
分子 | 名称: skeletal muscle actin / タイプ: protein_or_peptide / ID: 1 / Name.synonym: actin / 集合状態: helical filament / 組換発現: No / データベース: NCBI |
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由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 別称: Rabbit / 組織: Muscle / 細胞中の位置: Cytoplasm, cytoskeleton |
分子量 | 理論値: 41.8 KDa |
配列 | UniProtKB: Actin, alpha skeletal muscle |
-分子 #2: Metavinculin tail domain, residues 858-1129
分子 | 名称: Metavinculin tail domain, residues 858-1129 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: MVt / 集合状態: helical / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / Organelle: Focal adhesion / 細胞中の位置: Cytoplasmic |
分子量 | 理論値: 29.6 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) / 組換株: BL21(DE3) / 組換プラスミド: 2HR-T (Addgene #29718) |
配列 | UniProtKB: ビンキュリン |
-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 | らせん対称体再構成法 |
試料の集合状態 | filament |
-試料調製
濃度 | 0.0125 mg/mL |
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緩衝液 | pH: 7 / 詳細: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM imidazole |
グリッド | 詳細: 200 mesh 1.2 / 1.3 C-flat |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / 装置: LEICA EM GP 手法: 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar MVt was then applied and incubated for 60 seconds. 3 ...手法: 3 microliters of 0.3 micromolar actin was applied to the grid and incubated for 60 seconds at 25 degrees C. 3 microliters of 10 micromolar MVt was then applied and incubated for 60 seconds. 3 microliters of solution was removed, then an additional 3 microliters of MVt applied. After 60 seconds, 3 microliters of solution was removed, then the grid was blotted for 2 seconds before plunging. |
-電子顕微鏡法
顕微鏡 | FEI TECNAI 20 |
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電子線 | 加速電圧: 120 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 137615 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.0 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): 1.5 µm / 倍率(公称値): 100000 |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 100,000 times magnification. |
日付 | 2014年9月10日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 実像数: 671 / 平均電子線量: 25 e/Å2 |
-画像解析
CTF補正 | 詳細: FREALIGN (per segment) |
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最終 再構成 | 想定した対称性 - らせんパラメータ - Δz: 27.80 Å 想定した対称性 - らせんパラメータ - ΔΦ: 166.75 ° 想定した対称性 - らせんパラメータ - 軸対称性: C1 (非対称) アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 8.2 Å / 解像度の算出法: OTHER ソフトウェア - 名称: CTFFIND3, EMAN2/SPARX, FREALIGN |
詳細 | Multi-model IHRSR was performed using EMAN2 / SPARX to select for bound segments, followed by single-model IHRSR with EMAN2 / SPARX and final reconstruction with FREALIGN (fixed helical parameters). |
-原子モデル構築 1
初期モデル | PDB ID: Chain - Chain ID: A |
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ソフトウェア | 名称: Chimera, MDFF |
詳細 | Components were initially rigid body fit using Chimera, followed by flexible fitting with MDFF. |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
得られたモデル | PDB-3jbk: |