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基本情報
登録情報 | データベース: PDB / ID: 8h9e | |||||||||||||||
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タイトル | Human ATP synthase F1 domain, state 1 | |||||||||||||||
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![]() | MEMBRANE PROTEIN | |||||||||||||||
機能・相同性 | ![]() mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / positive regulation of proteolysis involved in protein catabolic process / Cristae formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / positive regulation of proteolysis involved in protein catabolic process / Cristae formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Mitochondrial protein import / negative regulation of ATP-dependent activity / negative regulation of hydrolase activity / oxidative phosphorylation / proton-transporting ATP synthase complex / cellular response to interleukin-7 / enzyme inhibitor activity / response to muscle activity / heme biosynthetic process / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / mitochondrial proton-transporting ATP synthase complex / MHC class I protein binding / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton transmembrane transport / Mitochondrial protein degradation / proton-transporting ATPase activity, rotational mechanism / reactive oxygen species metabolic process / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / cellular response to dexamethasone stimulus / generation of precursor metabolites and energy / mitochondrial membrane / regulation of intracellular pH / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / ADP binding / osteoblast differentiation / ATPase binding / angiogenesis / response to ethanol / protease binding / mitochondrial inner membrane / calmodulin binding / mitochondrial matrix / membrane raft / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane 類似検索 - 分子機能 | |||||||||||||||
生物種 | ![]() | |||||||||||||||
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: 2.53 Å | |||||||||||||||
![]() | Lai, Y. / Zhang, Y. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z. | |||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the human ATP synthase. 著者: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / ...著者: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong / ![]() ![]() 要旨: Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main ...Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of FF-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F and F motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex. | |||||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 524.8 KB | 表示 | ![]() |
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PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
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-検証レポート
文書・要旨 | ![]() | 2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2 MB | 表示 | |
XML形式データ | ![]() | 94.6 KB | 表示 | |
CIF形式データ | ![]() | 139.7 KB | 表示 | |
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 | ![]() 34564MC ![]() 8h9fC ![]() 8h9gC ![]() 8h9iC ![]() 8h9jC ![]() 8h9kC ![]() 8h9lC ![]() 8h9mC ![]() 8h9nC ![]() 8h9pC ![]() 8h9qC ![]() 8h9rC ![]() 8h9sC ![]() 8h9tC ![]() 8h9uC ![]() 8h9vC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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1 |
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要素
-ATP synthase subunit ... , 4種, 8分子 ABCEFDGO
#1: タンパク質 | 分子量: 55276.160 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) ![]() #2: タンパク質 | 分子量: 51821.965 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: タンパク質 | | 分子量: 30207.752 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() #4: タンパク質 | | 分子量: 20904.488 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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-タンパク質 , 1種, 1分子 J
#5: タンパク質 | 分子量: 9540.627 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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-非ポリマー , 3種, 10分子 ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#6: 化合物 | #7: 化合物 | ChemComp-MG / #8: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: Human ATP synthase / タイプ: COMPLEX / Entity ID: #1-#3, #5, #4 / 由来: NATURAL |
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分子量 | 値: 0.6 MDa / 実験値: YES |
由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 凍結剤: ETHANE |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2400 nm / 最小 デフォーカス(公称値): 1200 nm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) |
電子光学装置 | エネルギーフィルター名称: TFS Selectris X / エネルギーフィルタースリット幅: 10 eV |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.16_3549: / 分類: 精密化 | ||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.53 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 68388 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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