+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20721 | |||||||||
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タイトル | Isolated cofilin bound to an actin filament | |||||||||
マップデータ | Final unmasked map of isolated, bound cofilin segments selected from partially cofilin-decorated actin filaments. This map was low-pass filtered to 7.8 A and sharpened with a B-factor of -200. | |||||||||
試料 |
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キーワード | Cytoskeleton (細胞骨格) / STRUCTURAL PROTEIN (タンパク質) | |||||||||
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 / mesenchyme migration / myosin heavy chain binding / troponin I binding / filamentous actin / actin filament bundle / lamellipodium membrane / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / mitotic cytokinesis / 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 / マイクロフィラメント / 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 / マイクロフィラメント / Platelet degranulation / lamellipodium / cell body / 成長円錐 / 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 / 生体膜 / identical protein binding / 細胞核 / 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 | 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 AR / Bibeau JP / Schramm AC / Cao W / De La Cruz EM / Sindelar CV | |||||||||
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 | 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_20721.map.gz | 37.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20721-v30.xml emd-20721.xml | 20 KB 20 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20721.png | 158.1 KB | ||
マスクデータ | emd_20721_msk_1.map | 40.6 MB | マスクマップ | |
Filedesc metadata | emd-20721.cif.gz | 6.5 KB | ||
その他 | emd_20721_half_map_1.map.gz emd_20721_half_map_2.map.gz | 31.3 MB 31.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20721 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20721 | 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_20721.map.gz / 形式: CCP4 / 大きさ: 40.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Final unmasked map of isolated, bound cofilin segments selected from partially cofilin-decorated actin filaments. This map was low-pass filtered to 7.8 A and sharpened with a B-factor of -200. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.332 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
-マスク #1
ファイル | emd_20721_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 |
-ハーフマップ: Half map (odd) of isolated, bound cofilin segments...
ファイル | emd_20721_half_map_1.map | ||||||||||||
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注釈 | Half map (odd) of isolated, bound cofilin segments selected from partially cofilin-decorated actin filaments. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map (even) of isolated, bound cofilin segments...
ファイル | emd_20721_half_map_2.map | ||||||||||||
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注釈 | Half map (even) of isolated, bound cofilin segments selected from partially cofilin-decorated actin filaments. | ||||||||||||
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 rabbit skeletal actin with isolated, bound human cofilin-1
全体 | 名称: Complex of rabbit skeletal actin with isolated, bound human cofilin-1 |
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要素 |
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-超分子 #1: Complex of rabbit skeletal actin with isolated, bound human cofilin-1
超分子 | 名称: Complex of rabbit skeletal actin with isolated, bound human cofilin-1 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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-超分子 #2: Rabbit Skeletal Actin
超分子 | 名称: Rabbit Skeletal Actin / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) |
-超分子 #3: Human Cofilin-1
超分子 | 名称: Human Cofilin-1 / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Actin, alpha skeletal muscle
分子 | 名称: Actin, alpha skeletal muscle / タイプ: protein_or_peptide / ID: 1 / コピー数: 8 / 光学異性体: LEVO |
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由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) |
分子量 | 理論値: 42.096953 KDa |
配列 | 文字列: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...文字列: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F UniProtKB: Actin, alpha skeletal muscle |
-分子 #2: Cofilin-1
分子 | 名称: Cofilin-1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 18.532531 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MASGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYAT FVKMLPDKDC RYALYDATY ETKESKKEDL VFIFWAPESA PLKSKMIYAS SKDAIKKKLT GIKHELQANC YEEVKDRCTL AEKLGGSAVI S LEGKPL UniProtKB: Cofilin-1 |
-分子 #3: MAGNESIUM ION
分子 | 名称: MAGNESIUM ION / タイプ: ligand / ID: 3 / コピー数: 7 / 式: MG |
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分子量 | 理論値: 24.305 Da |
-分子 #4: ADENOSINE-5'-DIPHOSPHATE
分子 | 名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 4 / コピー数: 7 / 式: ADP |
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分子量 | 理論値: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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 | helical array |
-試料調製
緩衝液 | pH: 6.6 |
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凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 1117338 詳細: Both bare and cofilin-decorated segments were selected and initially refined together. |
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初期モデル | モデルのタイプ: OTHER |
初期 角度割当 | タイプ: NOT APPLICABLE |
最終 3次元分類 | クラス数: 2 / 平均メンバー数/クラス: 559000 詳細: Particle subtraction and masking were used to restrict classification to a single subunit per boxed segment. Particles were sorted into a bare and cofilin-decorated class. Filaments were then ...詳細: Particle subtraction and masking were used to restrict classification to a single subunit per boxed segment. Particles were sorted into a bare and cofilin-decorated class. Filaments were then searched for isolated, bound cofilin. |
最終 角度割当 | タイプ: NOT APPLICABLE |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 7.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF 詳細: Filament segments with isolated, bound cofilin were split into even and odd halves for FSC calculations. 使用した粒子像数: 8917 |