+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16965 | |||||||||
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タイトル | Mitochondrial complex I from Mus musculus in the active state | |||||||||
マップデータ | Cryo-EM map of mouse complex I sharpened with PHENIX auto-sharpen used for final model refinements | |||||||||
試料 |
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キーワード | Mitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / OXIDOREDUCTASE | |||||||||
機能・相同性 | 機能・相同性情報 response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / RHOG GTPase cycle / blastocyst hatching / circulatory system development ...response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / RHOG GTPase cycle / blastocyst hatching / circulatory system development / response to light intensity / protein insertion into mitochondrial inner membrane / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / cardiac muscle tissue development / : / [2Fe-2S] cluster assembly / oxygen sensor activity / adult walking behavior / respiratory chain complex I / cellular response to glucocorticoid stimulus / deoxynucleoside kinase activity / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of mitochondrial membrane potential / response to hydroperoxide / cellular respiration / ubiquinone-6 biosynthetic process / iron-sulfur cluster assembly / mitochondrial ribosome / adult behavior / dopamine metabolic process / positive regulation of ATP biosynthetic process / mitochondrial translation / NADH:ubiquinone reductase (H+-translocating) / positive regulation of execution phase of apoptosis / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / ubiquinone binding / acyl binding / neuron development / NADH dehydrogenase (ubiquinone) activity / cellular response to interferon-beta / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / negative regulation of reactive oxygen species biosynthetic process / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway / ATP metabolic process / : / tricarboxylic acid cycle / visual perception / aerobic respiration / Neutrophil degranulation / respiratory electron transport chain / reactive oxygen species metabolic process / mitochondrion organization / cerebellum development / neurogenesis / regulation of mitochondrial membrane potential / response to hormone / response to cocaine / fatty acid metabolic process / synaptic membrane / kidney development / muscle contraction / mitochondrial membrane / apoptotic signaling pathway / electron transport chain / sensory perception of sound / regulation of protein phosphorylation / ionotropic glutamate receptor binding / response to nicotine / response to hydrogen peroxide / multicellular organism growth / response to organic cyclic compound / mitochondrial intermembrane space / brain development / negative regulation of cell growth / cognition / 2 iron, 2 sulfur cluster binding / circadian rhythm / positive regulation of protein catabolic process / NAD binding / FMN binding / myelin sheath / nervous system development 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.39 Å | |||||||||
データ登録者 | Grba DN / Chung I / Bridges HR / Agip ANA / Hirst J | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I. 著者: Daniel N Grba / Injae Chung / Hannah R Bridges / Ahmed-Noor A Agip / Judy Hirst / 要旨: Respiratory complex I, a key enzyme in mammalian metabolism, captures the energy released by reduction of ubiquinone by NADH to drive protons across the inner mitochondrial membrane, generating the ...Respiratory complex I, a key enzyme in mammalian metabolism, captures the energy released by reduction of ubiquinone by NADH to drive protons across the inner mitochondrial membrane, generating the proton-motive force for ATP synthesis. Despite remarkable advances in structural knowledge of this complicated membrane-bound enzyme, its mechanism of catalysis remains controversial. In particular, how ubiquinone reduction is coupled to proton pumping and the pathways and mechanisms of proton translocation are contested. We present a 2.4-Å resolution cryo-EM structure of complex I from mouse heart mitochondria in the closed, active (ready-to-go) resting state, with 2945 water molecules modeled. By analyzing the networks of charged and polar residues and water molecules present, we evaluate candidate pathways for proton transfer through the enzyme, for the chemical protons for ubiquinone reduction, and for the protons transported across the membrane. Last, we compare our data to the predictions of extant mechanistic models, and identify key questions to answer in future work to test them. | |||||||||
履歴 |
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-構造の表示
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_16965.map.gz | 1.2 GB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16965-v30.xml emd-16965.xml | 76 KB 76 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16965_fsc.xml | 24.7 KB | 表示 | FSCデータファイル |
画像 | emd_16965.png | 125.1 KB | ||
マスクデータ | emd_16965_msk_1.map | 1.3 GB | マスクマップ | |
その他 | emd_16965_additional_1.map.gz emd_16965_additional_2.map.gz emd_16965_half_map_1.map.gz emd_16965_half_map_2.map.gz | 1.2 GB 1.2 GB 1.2 GB 1.2 GB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16965 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16965 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16965_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16965_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_16965_validation.xml.gz | 33 KB | 表示 | |
CIF形式データ | emd_16965_validation.cif.gz | 44.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16965 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16965 | HTTPS FTP |
-関連構造データ
関連構造データ | 8om1MC 8oltC M: このマップから作成された原子モデル 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
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 |
-マップ
ファイル | ダウンロード / ファイル: emd_16965.map.gz / 形式: CCP4 / 大きさ: 1.3 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Cryo-EM map of mouse complex I sharpened with PHENIX auto-sharpen used for final model refinements | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.6866 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | emd_16965_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Cryo-EM map of mouse complex I sharpened with...
ファイル | emd_16965_additional_1.map | ||||||||||||
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注釈 | Cryo-EM map of mouse complex I sharpened with RELION post-processing and an auto_b_highres value of 1.176 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Postprocessed but unfiltered map from the two half...
ファイル | emd_16965_additional_2.map | ||||||||||||
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注釈 | Postprocessed but unfiltered map from the two half maps of the final refinement. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map 1
ファイル | emd_16965_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half map 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: Unfiltered half map 2
ファイル | emd_16965_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Mitochondrial respiratory complex I
+超分子 #1: Mitochondrial respiratory 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
+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: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+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: DODECYL-BETA-D-MALTOSIDE
+分子 #46: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #47: IRON/SULFUR CLUSTER
+分子 #48: FE2/S2 (INORGANIC) CLUSTER
+分子 #49: FLAVIN MONONUCLEOTIDE
+分子 #50: SODIUM ION
+分子 #51: CARDIOLIPIN
+分子 #52: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #53: MAGNESIUM ION
+分子 #54: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+分子 #55: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #56: ZINC ION
+分子 #57: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+分子 #58: MYRISTIC ACID
+分子 #59: water
-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 |
-試料調製
濃度 | 4 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: UltrAuFoil / 材質: GOLD / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 90 sec. 詳細: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...詳細: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting | ||||||||||||
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: blot for 10 seconds before plunging. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 2674 / 平均露光時間: 2.53 sec. / 平均電子線量: 39.94 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 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): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 81000 |
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 |