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基本情報
登録情報 | データベース: EMDB / ID: EMD-4041 | |||||||||
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タイトル | Structure of mammalian respiratory Complex I, class3. | |||||||||
![]() | A map of third class of bovine Complex 1. | |||||||||
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機能・相同性 | ![]() Complex I biogenesis / RHOG GTPase cycle / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / oxygen sensor activity ...Complex I biogenesis / RHOG GTPase cycle / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / oxygen sensor activity / cellular respiration / Neutrophil degranulation / NADH dehydrogenase activity / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / neurogenesis / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / mitochondrial ATP synthesis coupled electron transport / 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 / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm 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: 5.6 Å | |||||||||
![]() | Vinothkumar KR / Zhu J / Hirst J | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of mammalian respiratory complex I. 著者: Jiapeng Zhu / Kutti R Vinothkumar / Judy Hirst / ![]() 要旨: Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive ...Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref. 1) contains 45 subunits, comprising 14 core subunits that house the catalytic machinery (and are conserved from bacteria to humans) and a mammalian-specific cohort of 31 supernumerary subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis. | |||||||||
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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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 164.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 74.2 KB 74.2 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.6 KB | 表示 | ![]() |
画像 | ![]() | 31.5 KB | ||
その他 | ![]() ![]() | 140.2 MB 140.2 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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 | A map of third class of bovine Complex 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: One of the half map from Relion
ファイル | emd_4041_half_map_1.map | ||||||||||||
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注釈 | One of the half map from Relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: the second half map from Relion
ファイル | emd_4041_half_map_2.map | ||||||||||||
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注釈 | the second half map from Relion | ||||||||||||
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 Complex I
+超分子 #1: Bovine Complex I
+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,NADH...
+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, NDUFA9
+分子 #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4
+分子 #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondr...
+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,NADH...
+分子 #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NAD...
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH...
+分子 #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #29: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [...
+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,NADH ...
+分子 #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8
+分子 #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH ...
+分子 #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH ...
+分子 #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH...
+分子 #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7
+分子 #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3
+分子 #45: IRON/SULFUR CLUSTER
+分子 #46: FE2/S2 (INORGANIC) CLUSTER
+分子 #47: FLAVIN MONONUCLEOTIDE
+分子 #48: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #49: ZINC ION
-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 | 3.5 mg/mL |
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緩衝液 | pH: 8 / 構成要素 - 濃度: 150.0 mM / 構成要素 - 式: NaCl / 構成要素 - 名称: sodium chloride |
グリッド | モデル: Quantifoil / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 支持フィルム - Film thickness: 15.0 nm / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR 詳細: holey carbon grids were placed on a filter paper in a glass petridish and pumped for around 5 minutes to remove any residual moisture. the glow of the plasma was observed and glow discharged when it was purple |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: HOMEMADE PLUNGER 詳細: The specimen was vitrified in an environmental plunge-freeze apparatus, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged.. |
詳細 | Enzyme was purified from bovine heart mitochondria. The detergent used for the final step is cymal-7. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 85.0 K / 最高: 85.0 K |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / デジタル化 - サンプリング間隔: 14.0 µm / デジタル化 - 画像ごとのフレーム数: 1-34 / 平均露光時間: 2.0 sec. / 平均電子線量: 35.0 e/Å2 詳細: Images were collected in movie mode at 17 frames per second. Thus each frame has ~1.0 e/A2s |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 70.0 µm / 倍率(補正後): 105263 / 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): 5.5 µm / 最小 デフォーカス(公称値): 1.8 µm / 倍率(公称値): 59000 |
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 | The model from Class1 (D_1200000497) was used for rigid body fitting. The B-factor for individual atoms is carried over from class 1 and doesn't mean anything. |
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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-5ldx: |