+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19146 | |||||||||
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タイトル | Open Complex I from murine liver | |||||||||
マップデータ | combined map | |||||||||
試料 |
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キーワード | respiratory chain complex / mammalian mitochondria / MEMBRANE PROTEIN / ELECTRON TRANSPORT | |||||||||
機能・相同性 | 機能・相同性情報 response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development ...response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / response to light intensity / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone-6 biosynthetic process / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / cardiac muscle tissue development / : / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / adult walking behavior / oxygen sensor activity / cellular response to glucocorticoid stimulus / response to hydroperoxide / positive regulation of mitochondrial membrane potential / cellular respiration / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / adult behavior / mitochondrial translation / positive regulation of ATP biosynthetic process / dopamine metabolic process / positive regulation of execution phase of apoptosis / NADH:ubiquinone reductase (H+-translocating) / : / ubiquinone binding / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / cellular response to interferon-beta / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / ATP synthesis coupled electron transport / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / muscle contraction / negative regulation of reactive oxygen species biosynthetic process / ATP metabolic process / extrinsic apoptotic signaling pathway / tricarboxylic acid cycle / visual perception / aerobic respiration / ionotropic glutamate receptor binding / response to hormone / Neutrophil degranulation / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / cerebellum development / regulation of mitochondrial membrane potential / kidney development / mitochondrion organization / response to cocaine / fatty acid metabolic process / cognition / synaptic membrane / mitochondrial membrane / apoptotic signaling pathway / sensory perception of sound / electron transport chain / response to nicotine / regulation of protein phosphorylation / response to hydrogen peroxide / multicellular organism growth / brain development / response to organic cyclic compound / negative regulation of cell growth / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / positive regulation of protein catabolic process / NAD binding / FMN binding / myelin sheath / nervous system development / 4 iron, 4 sulfur cluster binding 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: 3.0 Å | |||||||||
データ登録者 | Vercellino I / Sazanov LA | |||||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: SCAF1 drives the compositional diversity of mammalian respirasomes. 著者: Irene Vercellino / Leonid A Sazanov / 要旨: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies ...Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIIICIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions. #1: ジャーナル: Acta Crystallogr., Sect. D: Biol. Cristallogr. 年: 2018 タイトル: Real-space refinement in PHENIX for cryo-EM and crystallography 著者: Afonine PV / Adams PD | |||||||||
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_19146.map.gz | 6.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19146-v30.xml emd-19146.xml | 66.8 KB 66.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19146_fsc.xml | 21.1 KB | 表示 | FSCデータファイル |
画像 | emd_19146.png | 93.8 KB | ||
Filedesc metadata | emd-19146.cif.gz | 14.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19146 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19146 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19146_validation.pdf.gz | 510 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19146_full_validation.pdf.gz | 509.6 KB | 表示 | |
XML形式データ | emd_19146_validation.xml.gz | 13.4 KB | 表示 | |
CIF形式データ | emd_19146_validation.cif.gz | 19.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19146 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19146 | HTTPS FTP |
-関連構造データ
関連構造データ | 8rgqMC 8pw5C 8pw6C 8pw7C 8rgpC 8rgrC 8rgtC C: 同じ文献を引用 (文献) 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 | 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_19146.map.gz / 形式: CCP4 / 大きさ: 32.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | combined map | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 これらの図は立方格子座標系で作成されたものです | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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
-試料の構成要素
+全体 : Open Complex I from murine liver
+超分子 #1: Open Complex I from murine liver
+分子 #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+分子 #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+分子 #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+分子 #4: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #5: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #6: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+分子 #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+分子 #8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+分子 #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+分子 #10: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #11: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #12: Acyl carrier protein, mitochondrial
+分子 #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+分子 #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+分子 #17: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+分子 #18: NADH-ubiquinone oxidoreductase chain 3
+分子 #19: NADH-ubiquinone oxidoreductase chain 1
+分子 #20: NADH-ubiquinone oxidoreductase chain 6
+分子 #21: NADH-ubiquinone oxidoreductase chain 4L
+分子 #22: NADH-ubiquinone oxidoreductase chain 5
+分子 #23: NADH-ubiquinone oxidoreductase chain 4
+分子 #24: NADH-ubiquinone oxidoreductase chain 2
+分子 #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+分子 #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #31: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #32: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+分子 #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+分子 #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+分子 #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+分子 #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+分子 #42: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #45: IRON/SULFUR CLUSTER
+分子 #46: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #47: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #48: FE2/S2 (INORGANIC) CLUSTER
+分子 #49: FLAVIN MONONUCLEOTIDE
+分子 #50: POTASSIUM ION
+分子 #51: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #52: ZINC ION
+分子 #53: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+分子 #54: CARDIOLIPIN
+分子 #55: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+分子 #56: MAGNESIUM 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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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.3 mg/mL | ||||||||||||
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緩衝液 | pH: 7.7 構成要素:
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グリッド | モデル: Quantifoil R0.6/1 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 1 | ||||||||||||
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: FEI VITROBOT MARK IV |
-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: 9453 / 平均露光時間: 4.4 sec. / 平均電子線量: 80.0 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: 50.0 µm / 最大 デフォーカス(補正後): 2.5 µm / 最小 デフォーカス(補正後): 0.5 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): 1.0 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 |