+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6d8c | |||||||||
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タイトル | Cryo-EM structure of FLNaABD E254K bound to phalloidin-stabilized F-actin | |||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN (タンパク質) / Actin-binding domain / Actin crosslinker | |||||||||
機能・相同性 | 機能・相同性情報 regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / formation of radial glial scaffolds / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation ...regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / formation of radial glial scaffolds / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / OAS antiviral response / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / Striated Muscle Contraction / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / Cell-extracellular matrix interactions / positive regulation of potassium ion transmembrane transport / early endosome to late endosome transport / apical dendrite / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / negative regulation of transcription by RNA polymerase I / Fc-gamma receptor I complex binding / wound healing, spreading of cells / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / receptor clustering / positive regulation of axon regeneration / actin filament bundle / SMAD binding / RHO GTPases activate PAKs / skeletal muscle thin filament assembly / 刷子縁 / striated muscle thin filament / semaphorin-plexin signaling pathway / cilium assembly / mitotic spindle assembly / potassium channel regulator activity / 上皮間葉転換 / blood vessel remodeling / skeletal muscle fiber development / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / stress fiber / regulation of cell migration / release of sequestered calcium ion into cytosol / protein kinase C binding / dendritic shaft / G protein-coupled receptor binding / マイクロフィラメント / protein localization to plasma membrane / synapse organization / 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 / mRNA transcription by RNA polymerase II / establishment of protein localization / ゴルジ体 / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / cerebral cortex development / 血小板 / Z disc / small GTPase binding / kinase binding / positive regulation of protein import into nucleus / actin filament binding / cell-cell junction / マイクロフィラメント / negative regulation of neuron projection development / Platelet degranulation / GTPase binding / toxin activity / perikaryon / actin cytoskeleton organization / postsynapse / 血管新生 / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / transmembrane transporter binding / protein stabilization / hydrolase activity / cadherin binding / focal adhesion / glutamatergic synapse / 核小体 / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / ATP binding / 生体膜 / 細胞核 / 細胞膜 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) Gallus gallus (ニワトリ) Amanita phalloides (タマゴテングタケ) | |||||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 3.54 Å | |||||||||
データ登録者 | Iwamoto, D.V. / Huehn, A.R. / Simon, B. / Huet-Calderwood, C. / Baldassarre, M. / Sindelar, C.V. / Calderwood, D.A. | |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2018 タイトル: Structural basis of the filamin A actin-binding domain interaction with F-actin. 著者: Daniel V Iwamoto / Andrew Huehn / Bertrand Simon / Clotilde Huet-Calderwood / Massimiliano Baldassarre / Charles V Sindelar / David A Calderwood / 要旨: Actin-cross-linking proteins assemble actin filaments into higher-order structures essential for orchestrating cell shape, adhesion, and motility. Missense mutations in the tandem calponin homology ...Actin-cross-linking proteins assemble actin filaments into higher-order structures essential for orchestrating cell shape, adhesion, and motility. Missense mutations in the tandem calponin homology domains of their actin-binding domains (ABDs) underlie numerous genetic diseases, but a molecular understanding of these pathologies is hampered by the lack of high-resolution structures of any actin-cross-linking protein bound to F-actin. Here, taking advantage of a high-affinity, disease-associated mutant of the human filamin A (FLNa) ABD, we combine cryo-electron microscopy and functional studies to reveal at near-atomic resolution how the first calponin homology domain (CH1) and residues immediately N-terminal to it engage actin. We further show that reorientation of CH2 relative to CH1 is required to avoid clashes with actin and to expose F-actin-binding residues on CH1. Our data explain localization of disease-associated loss-of-function mutations to FLNaCH1 and gain-of-function mutations to the regulatory FLNaCH2. Sequence conservation argues that this provides a general model for ABD-F-actin binding. | |||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6d8c.cif.gz | 854.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6d8c.ent.gz | 711.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6d8c.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d8/6d8c ftp://data.pdbj.org/pub/pdb/validation_reports/d8/6d8c | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 34476.250 Da / 分子数: 5 / 断片: UNP residues 1-278 / 変異: E254K / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FLNA, FLN, FLN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta / 参照: UniProt: P21333 #2: タンパク質 | 分子量: 41862.613 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 組織: Breast / 参照: UniProt: P68139 #3: タンパク質・ペプチド | #4: 化合物 | ChemComp-ADP / #5: 化合物 | ChemComp-MG / |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 | 名称: Helical complex of FLNaABD E254K bound to phalloidin-stabilized F-actin タイプ: COMPLEX / Entity ID: #1-#3 / 由来: MULTIPLE SOURCES |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) / 株: Rosetta |
緩衝液 | pH: 8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 105000 X / 倍率(補正後): 37500 X / 最大 デフォーカス(公称値): 2900 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE |
試料ホルダ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 12 sec. / 電子線照射量: 50 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 2 / 実像数: 2140 詳細: Micrographs from only one of the grids were used in the reconstruction. From that grid, only micrographs where Gctf detected signal at resolutions better than 4A were used in the reconstruction (~15%). |
画像スキャン | 動画フレーム数/画像: 40 / 利用したフレーム数/画像: 1-40 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: -166.73 ° / 軸方向距離/サブユニット: 27.54 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 67000 | ||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.54 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 67000 / 対称性のタイプ: HELICAL | ||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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