+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6uby | |||||||||
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タイトル | Isolated cofilin bound to an actin filament | |||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN / Cytoskeleton | |||||||||
機能・相同性 | 機能・相同性情報 actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / cytoskeletal motor activator activity ...actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / lamellipodium membrane / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / mitotic cytokinesis / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / cytoskeleton organization / EPHB-mediated forward signaling / actin filament polymerization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / actin filament / 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 / response to virus / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / nuclear matrix / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / growth cone / cell body / actin cytoskeleton organization / vesicle / hydrolase activity / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / magnesium ion binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) Oryctolagus cuniculus (ウサギ) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.5 Å | |||||||||
データ登録者 | Huehn, A.R. / Bibeau, J.P. / Schramm, A.C. / Cao, W. / De La Cruz, E.M. / Sindelar, C.V. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2020 タイトル: Structures of cofilin-induced structural changes reveal local and asymmetric perturbations of actin filaments. 著者: Andrew R Huehn / Jeffrey P Bibeau / Anthony C Schramm / Wenxiang Cao / Enrique M De La Cruz / Charles V Sindelar / 要旨: Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with ...Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with positive cooperativity, forming clusters of contiguously bound cofilin along the filament lattice. Filament severing occurs preferentially at boundaries between bare and cofilin-decorated (cofilactin) segments and is biased at 1 side of a cluster. A molecular understanding of cooperative binding and filament severing has been impeded by a lack of structural data describing boundaries. Here, we apply methods for analyzing filament cryo-electron microscopy (cryo-EM) data at the single subunit level to directly investigate the structure of boundaries within partially decorated cofilactin filaments. Subnanometer resolution maps of isolated, bound cofilin molecules and an actin-cofilactin boundary indicate that cofilin-induced actin conformational changes are local and limited to subunits directly contacting bound cofilin. An isolated, bound cofilin compromises longitudinal filament contacts of 1 protofilament, consistent with a single cofilin having filament-severing activity. An individual, bound phosphomimetic (S3D) cofilin with weak severing activity adopts a unique binding mode that does not perturb actin structure. Cofilin clusters disrupt both protofilaments, consistent with a higher severing activity at boundaries compared to single cofilin. Comparison of these structures indicates that this disruption is substantially greater at pointed end sides of cofilactin clusters than at the barbed end. These structures, with the distribution of bound cofilin clusters, suggest that maximum binding cooperativity is achieved when 2 cofilins occupy adjacent sites. These results reveal the structural origins of cooperative cofilin binding and actin filament severing. | |||||||||
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 | 6uby.cif.gz | 473.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6uby.ent.gz | 391.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6uby.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
文書・要旨 | 6uby_validation.pdf.gz | 1.8 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6uby_full_validation.pdf.gz | 1.9 MB | 表示 | |
XML形式データ | 6uby_validation.xml.gz | 87.7 KB | 表示 | |
CIF形式データ | 6uby_validation.cif.gz | 121.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ub/6uby ftp://data.pdbj.org/pub/pdb/validation_reports/ub/6uby | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 42096.953 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: P68135 #2: タンパク質 | | 分子量: 18532.531 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CFL1, CFL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P23528 #3: 化合物 | ChemComp-MG / #4: 化合物 | ChemComp-ADP / 構成要素の詳細 | The major close contacts arise because the authors have fitted rigid-body atomic models into low ...The major close contacts arise because the authors have fitted rigid-body atomic models into low resolution maps | 研究の焦点であるリガンドがあるか | N | 配列の詳細 | The molecules in the experiments were: Rabbit actin (UniProt P68135) and Human cofilin-1 (UniProt ...The molecules in the experiments were: Rabbit actin (UniProt P68135) and Human cofilin-1 (UniProt P23528), however the sequences modeled in the coordinates correspond to the sequences from Chicken actin and Chicken cofilin-2 since those were pdb models of homolog molecules used to fit into the cryo-EM density maps. | |
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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: HELICAL ARRAY / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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分子量 | 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: Escherichia coli (大腸菌) | ||||||||||||||||||||||||
緩衝液 | pH: 6.6 | ||||||||||||||||||||||||
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 FIELD |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア | 名称: UCSF Chimera / カテゴリ: モデルフィッティング | ||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1117338 詳細: Both bare and cofilin-decorated segments were selected and initially refined together. | ||||||||||||||||||
3次元再構成 | 解像度: 7.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 8917 詳細: Filament segments with isolated, bound cofilin were split into even and odd halves for FSC calculations. 対称性のタイプ: POINT | ||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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