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基本情報
登録情報 | データベース: EMDB / ID: EMD-4345 | ||||||||||||
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タイトル | Mouse mitochondrial complex I in the active state | ||||||||||||
![]() | Mouse mitochondrial complex I in the active state | ||||||||||||
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![]() | Complex I / mitochondria / proton pump / membrane protein / oxidoreductase | ||||||||||||
機能・相同性 | ![]() Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / respiratory system process ...Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / cellular response to oxygen levels / response to light intensity / mesenchymal stem cell proliferation / respiratory chain complex / mitochondrial [2Fe-2S] assembly complex / reproductive system development / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / mesenchymal stem cell differentiation / circulatory system development / negative regulation of non-canonical NF-kappaB signal transduction / cardiac muscle tissue development / neural precursor cell proliferation / positive regulation of mitochondrial membrane potential / [2Fe-2S] cluster assembly / adult walking behavior / oxygen sensor activity / response to hydroperoxide / cellular response to glucocorticoid stimulus / stem cell division / NADH dehydrogenase activity / iron-sulfur cluster assembly / mitochondrial ATP synthesis coupled electron transport / dopamine metabolic process / NADH:ubiquinone reductase (H+-translocating) / adult behavior / positive regulation of ATP biosynthetic process / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / positive regulation of execution phase of apoptosis / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / tricarboxylic acid cycle / neurogenesis / Neutrophil degranulation / regulation of mitochondrial membrane potential / visual perception / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / cerebellum development / respiratory electron transport chain / response to nicotine / response to cocaine / mitochondrion organization / DNA damage response, signal transduction by p53 class mediator / kidney development / fatty acid metabolic process / response to hydrogen peroxide / sensory perception of sound / monooxygenase activity / electron transport chain / circadian rhythm / mitochondrial membrane / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / cognition / multicellular organism growth / NAD binding / positive regulation of protein catabolic process / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / myelin sheath / 4 iron, 4 sulfur cluster binding / response to oxidative stress / neuron apoptotic process / response to ethanol / gene expression / in utero embryonic development / response to hypoxia / electron transfer activity / mitochondrial inner membrane / nuclear speck / nuclear body / mitochondrial matrix / inflammatory response 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: 3.3 Å | ||||||||||||
![]() | Agip ANA / Blaza JN | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM structures of complex I from mouse heart mitochondria in two biochemically defined states. 著者: Ahmed-Noor A Agip / James N Blaza / Hannah R Bridges / Carlo Viscomi / Shaun Rawson / Stephen P Muench / Judy Hirst / ![]() 要旨: Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian ...Complex I (NADH:ubiquinone oxidoreductase) uses the reducing potential of NADH to drive protons across the energy-transducing inner membrane and power oxidative phosphorylation in mammalian mitochondria. Recent cryo-EM analyses have produced near-complete models of all 45 subunits in the bovine, ovine and porcine complexes and have identified two states relevant to complex I in ischemia-reperfusion injury. Here, we describe the 3.3-Å structure of complex I from mouse heart mitochondria, a biomedically relevant model system, in the 'active' state. We reveal a nucleotide bound in subunit NDUFA10, a nucleoside kinase homolog, and define mechanistically critical elements in the mammalian enzyme. By comparisons with a 3.9-Å structure of the 'deactive' state and with known bacterial structures, we identify differences in helical geometry in the membrane domain that occur upon activation or that alter the positions of catalytically important charged residues. Our results demonstrate the capability of cryo-EM analyses to challenge and develop mechanistic models for mammalian complex I. | ||||||||||||
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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マップデータ | ![]() | 325.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 77.1 KB 77.1 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 16 KB | 表示 | ![]() |
画像 | ![]() | 89 KB | ||
Filedesc metadata | ![]() | 15.6 KB | ||
その他 | ![]() ![]() | 279.4 MB 278.3 MB | ||
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文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 23.3 KB | 表示 | |
CIF形式データ | ![]() | 31.3 KB | 表示 | |
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-関連構造データ
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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 | Mouse mitochondrial complex I in the active state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 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
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試料の構成要素
+全体 : Mitochondrial complex I from mouse in the active state
+超分子 #1: Mitochondrial complex I from mouse in the active state
+分子 #1: NADH-ubiquinone oxidoreductase chain 3
+分子 #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+分子 #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+分子 #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+分子 #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+分子 #8: NADH-ubiquinone oxidoreductase chain 1
+分子 #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+分子 #10: NADH-ubiquinone oxidoreductase chain 6
+分子 #11: NADH-ubiquinone oxidoreductase chain 4L
+分子 #12: NADH-ubiquinone oxidoreductase chain 5
+分子 #13: NADH-ubiquinone oxidoreductase chain 4
+分子 #14: NADH-ubiquinone oxidoreductase chain 2
+分子 #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+分子 #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+分子 #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #20: Acyl carrier protein, mitochondrial
+分子 #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+分子 #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #24: MCG5603
+分子 #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+分子 #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+分子 #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+分子 #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+分子 #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+分子 #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+分子 #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+分子 #45: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #46: IRON/SULFUR CLUSTER
+分子 #47: FE2/S2 (INORGANIC) CLUSTER
+分子 #48: FLAVIN MONONUCLEOTIDE
+分子 #49: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #50: CARDIOLIPIN
+分子 #51: ADENOSINE-5'-DIPHOSPHATE
+分子 #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #53: ZINC ION
+分子 #54: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
-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 | 5 mg/mL | ||||||||||||
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緩衝液 | pH: 7.14 構成要素:
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グリッド | モデル: Quantifoil UltrAuFoil / 材質: GOLD / メッシュ: 300 詳細: Gold was PEGylated prior to use in anaerobic ethanol in 5mM SPT-11P6 (Sensopath Technologies) for two days 0.6/1 holes | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: 8-16s blotting.. | ||||||||||||
詳細 | Peak fraction from a gel filtration column- monodisperse and not concentrated |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS エネルギーフィルター - エネルギー下限: 0 eV エネルギーフィルター - エネルギー上限: 20 eV |
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 / デジタル化 - 画像ごとのフレーム数: 1-12 / 撮影したグリッド数: 1 / 平均露光時間: 10.0 sec. / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 47600 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.1 µm / 最小 デフォーカス(公称値): 1.5 µm |
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
詳細 | Used default paramteres in phenix.real_space_refine |
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精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
得られたモデル | ![]() PDB-6g2j: |