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基本情報
登録情報 | データベース: EMDB / ID: EMD-11039 | |||||||||
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タイトル | bovine ATP synthase F1-peripheral stalk domain, state 2 | |||||||||
![]() | State 2 half mask 1 | |||||||||
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機能・相同性 | ![]() angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / proton-transporting ATP synthase complex / heme biosynthetic process / : / : / : / : / Mitochondrial protein degradation / : / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / aerobic respiration / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.29 Å | |||||||||
![]() | Spikes T / Montgomery MG / Walker JE | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the dimeric ATP synthase from bovine mitochondria. 著者: Tobias E Spikes / Martin G Montgomery / John E Walker / ![]() 要旨: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 446.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 33.6 KB 33.6 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 17.7 KB | 表示 | ![]() |
画像 | ![]() | 49.1 KB | ||
マスクデータ | ![]() | 476.8 MB | ![]() | |
その他 | ![]() ![]() | 385.4 MB 385.6 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6z1rMC ![]() 6yy0C ![]() 6z1uC ![]() 6zbbC ![]() 6zg7C ![]() 6zg8C ![]() 6zikC ![]() 6ziqC ![]() 6zitC ![]() 6ziuC ![]() 6zmrC ![]() 6znaC ![]() 6zpoC ![]() 6zqmC ![]() 6zqnC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | State 2 half mask 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.048 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 | ![]() | ||||||||||||
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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: State 2 half map 2
ファイル | emd_11039_half_map_1.map | ||||||||||||
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注釈 | State 2 half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: atp synthase monomer mask
ファイル | emd_11039_half_map_2.map | ||||||||||||
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注釈 | atp synthase monomer mask | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
+超分子 #1: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
+超分子 #2: ATP synthase F1 domain
+超分子 #3: ATP synthase peripheral stalk
+超分子 #4: ATPase inhibitor, mitochondrial
+分子 #1: ATP synthase subunit alpha, mitochondrial
+分子 #2: ATP synthase subunit beta, mitochondrial
+分子 #3: ATP synthase subunit gamma, mitochondrial
+分子 #4: ATP synthase subunit delta, mitochondrial
+分子 #5: ATP synthase subunit epsilon, mitochondrial
+分子 #6: ATPase inhibitor, mitochondrial
+分子 #7: ATP synthase F(0) complex subunit C2, mitochondrial
+分子 #8: ATP synthase subunit O, mitochondrial
+分子 #9: ATP synthase F(0) complex subunit B1, mitochondrial
+分子 #10: ATP synthase-coupling factor 6, mitochondrial
+分子 #11: ADENOSINE-5'-TRIPHOSPHATE
+分子 #12: MAGNESIUM ION
+分子 #13: ADENOSINE-5'-DIPHOSPHATE
+分子 #14: water
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 4.5 mg/mL |
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緩衝液 | pH: 7.4 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 294 K / 装置: FEI VITROBOT MARK IV 詳細: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting.. |
詳細 | Nickel affinity purified filled by gel filtration |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 検出モード: COUNTING / 平均露光時間: 12.0 sec. / 平均電子線量: 4.6 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
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 |
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画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||||||
得られたモデル | ![]() PDB-6z1r: |