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データを開く
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基本情報
| 登録情報 | データベース: EMDB / ID: EMD-4356 | ||||||||||||
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| タイトル | Mouse mitochondrial complex I in the deactive state | ||||||||||||
マップデータ | Mouse mitochondrial complex I in the deactive state | ||||||||||||
試料 |
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キーワード | Complex I / mitochondria / proton pump / membrane protein / oxidoreductase | ||||||||||||
| 機能・相同性 | 機能・相同性情報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 / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / Respiratory electron transport / protein insertion into mitochondrial inner membrane ...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 / Mitochondrial ribosome-associated quality control / Mitochondrial translation termination / Respiratory electron transport / protein insertion into mitochondrial inner membrane / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / response to light intensity / protein lipoylation / mesenchymal stem cell proliferation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / reproductive system development / ubiquinone biosynthetic process / mitochondrial large ribosomal subunit binding / mitochondrial [2Fe-2S] assembly complex / gliogenesis / respiratory chain complex / mesenchymal stem cell differentiation / circulatory system development / negative regulation of non-canonical NF-kappaB signal transduction / cellular respiration / response to hydroperoxide / adult walking behavior / cardiac muscle tissue development / positive regulation of mitochondrial membrane potential / neural precursor cell proliferation / oxygen sensor activity / [2Fe-2S] cluster assembly / cellular response to glucocorticoid stimulus / stem cell division / iron-sulfur cluster assembly / NADH:ubiquinone reductase (H+-translocating) / dopamine metabolic process / ubiquinone binding / adult behavior / positive regulation of ATP biosynthetic process / mitochondrial ATP synthesis coupled electron transport / electron transport coupled proton transport / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / acyl binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / positive regulation of execution phase of apoptosis / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / response to cAMP / neuron development / quinone binding / ATP synthesis coupled electron transport / cellular response to interferon-beta / tricarboxylic acid cycle / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / Neutrophil degranulation / response to hormone / visual perception / reactive oxygen species metabolic process / neurogenesis / ionotropic glutamate receptor binding / muscle contraction / cerebellum development / aerobic respiration / regulation of mitochondrial membrane potential / respiratory electron transport chain / synaptic membrane / response to nicotine / response to cocaine / DNA damage response, signal transduction by p53 class mediator / kidney development / response to hydrogen peroxide / monooxygenase activity / mitochondrion organization / sensory perception of sound / electron transport chain / circadian rhythm / fatty acid metabolic process / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / cognition / multicellular organism growth / mitochondrial membrane / NAD binding / cellular senescence / positive regulation of protein catabolic process / FMN binding / nervous system development / myelin sheath 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: 3.9 Å | ||||||||||||
データ登録者 | Agip ANA / Blaza JN | ||||||||||||
| 資金援助 | 英国, 3件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2018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: SurfView Molmil Jmol/JSmol |
| 添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
| マップデータ | emd_4356.map.gz | 172 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-4356-v30.xml emd-4356.xml | 70.5 KB 70.5 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_4356_fsc.xml | 12.9 KB | 表示 | FSCデータファイル |
| 画像 | emd_4356.png | 97.2 KB | ||
| Filedesc metadata | emd-4356.cif.gz | 14.3 KB | ||
| その他 | emd_4356_half_map_1.map.gz emd_4356_half_map_2.map.gz | 146.1 MB 146 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4356 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4356 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 6g72MC ![]() 4345C ![]() 6g2jC 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 | |
| 電子顕微鏡画像生データ | EMPIAR-10604 (タイトル: Single particle cryo-EM dataset of Mus musculus mitochondrial complex I in the deactive stateData size: 2.7 TB Data #1: Single particle cryo-EM dataset of Mus musculus mitochondrial complex I in the deactive state [micrographs - multiframe]) |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_4356.map.gz / 形式: CCP4 / 大きさ: 184 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 注釈 | Mouse mitochondrial complex I in the deactive state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| ボクセルのサイズ | X=Y=Z: 1.33 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
-ハーフマップ: Half-1
| ファイル | emd_4356_half_map_1.map | ||||||||||||
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| 注釈 | Half-1 | ||||||||||||
| 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-2
| ファイル | emd_4356_half_map_2.map | ||||||||||||
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| 注釈 | Half-2 | ||||||||||||
| 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 : Mitochondrial complex I from mouse in the deactive state
+超分子 #1: Mitochondrial complex I from mouse in the deactive 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: IRON/SULFUR CLUSTER
+分子 #46: FE2/S2 (INORGANIC) CLUSTER
+分子 #47: FLAVIN MONONUCLEOTIDE
+分子 #48: ADENOSINE-5'-DIPHOSPHATE
+分子 #49: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #50: ZINC ION
+分子 #51: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+分子 #52: ACETYL GROUP
-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 | particle |
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試料調製
| 濃度 | 3 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. The complex was put into the deactive state by heating at 37degC for 30 mins before isolation in detergent. |
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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: 1-30 / 撮影したグリッド数: 1 / 平均露光時間: 15.0 sec. / 平均電子線量: 50.0 e/Å2 |
| 電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
| 電子光学系 | 倍率(補正後): 37600 / 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): 3.4 µm / 最小 デフォーカス(公称値): 2.2 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-6g72: |
ムービー
コントローラー
万見について



キーワード
データ登録者
英国, 3件
引用
UCSF Chimera











































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