+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7zd6 | ||||||
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タイトル | Complex I from Ovis aries, at pH7.4, Open state | ||||||
要素 |
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キーワード | PROTON TRANSPORT / Complex I / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein / Quinone | ||||||
機能・相同性 | 機能・相同性情報 myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity ...myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / positive regulation of myoblast differentiation / quinone binding / electron transport coupled proton transport / : / positive regulation of lamellipodium assembly / ATP synthesis coupled electron transport / ATP metabolic process / mitochondrial ATP synthesis coupled electron transport / transcription coregulator activity / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / circadian rhythm / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix / chromatin / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | Ovis aries (ヒツジ) | ||||||
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: 3.16 Å | ||||||
データ登録者 | Sazanov, L. / Petrova, O. | ||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: Nature / 年: 2022 タイトル: A universal coupling mechanism of respiratory complex I. 著者: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov / 要旨: Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7zd6.cif.gz | 1.6 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7zd6.ent.gz | 1.3 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7zd6.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/zd/7zd6 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zd6 | HTTPS FTP |
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-関連構造データ
関連構造データ | 14637MC 7p61C 7p62C 7p63C 7p64C 7p69C 7p7cC 7p7eC 7p7jC 7p7kC 7p7lC 7p7mC 7z7rC 7z7sC 7z7tC 7z7vC 7z80C 7z83C 7z84C 7zc5C 7zciC 7zdhC 7zdjC 7zdmC 7zdpC 7zebC 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+NADH-ubiquinone oxidoreductase chain ... , 7種, 7分子 AHJKLMN
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 9種, 9分子 VYkmqefgi
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 8種, 8分子 Wnstuvwy
+タンパク質 , 5種, 6分子 XjZz34
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6種, 6分子 l569bc
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2種, 2分子 ox
+NADH:ubiquinone oxidoreductase subunit ... , 2種, 2分子 pd
+Mitochondrial complex I, ... , 2種, 2分子 rh
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3種, 3分子 12a
+非ポリマー , 13種, 38分子
+詳細
-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 |
-試料調製
構成要素 | 名称: Complex I from Ovis aries, at pH7.4, Open state / タイプ: COMPLEX / Entity ID: #1-#44 / 由来: NATURAL |
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分子量 | 値: 1 MDa / 実験値: YES |
由来(天然) | 生物種: Ovis aries (ヒツジ) |
緩衝液 | pH: 7.4 |
試料 | 濃度: 3 mg/ml / 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 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
顕微鏡 | モデル: TFS GLACIOS |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 120000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 平均露光時間: 3.3 sec. / 電子線照射量: 90 e/Å2 フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: dev_4092: / 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: 3.16 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 113712 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6ZKE | ||||||||||||||||||||||||
拘束条件 |
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