+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17989 | |||||||||
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タイトル | CS respirasome from murine liver | |||||||||
マップデータ | composite map | |||||||||
試料 |
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キーワード | Respiratory chain super complex / mammalian mitochondria / MEMBRANE PROTEIN (膜タンパク質) | |||||||||
機能・相同性 | 機能・相同性情報 Mitochondrial protein degradation / subthalamus development / pons development / response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / TP53 Regulates Metabolic Genes / reproductive system development / Mitochondrial protein import / Respiratory electron transport ...Mitochondrial protein degradation / subthalamus development / pons development / response to injury involved in regulation of muscle adaptation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / TP53 Regulates Metabolic Genes / reproductive system development / Mitochondrial protein import / Respiratory electron transport / Glyoxylate metabolism and glycine degradation / cerebellar Purkinje cell layer development / RHOG GTPase cycle / respiratory system process / response to light intensity / protein insertion into mitochondrial inner membrane / blastocyst hatching / circulatory system development / pyramidal neuron development / respiratory chain complex IV assembly / response to mercury ion / thalamus development / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / respiratory chain complex IV / psychomotor behavior / mitochondrial respiratory chain complex III assembly / cellular response to oxygen levels / iron-sulfur cluster assembly complex / regulation of oxidative phosphorylation / mitochondrial large ribosomal subunit binding / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / gliogenesis / cardiac muscle tissue development / response to alkaloid / neural precursor cell proliferation / ubiquinone-6 biosynthetic process / シトクロムcオキシダーゼ / mitochondrial respirasome / quinol-cytochrome-c reductase / [2Fe-2S] cluster assembly / ubiquinol-cytochrome-c reductase activity / oxygen sensor activity / adult walking behavior / negative regulation of non-canonical NF-kappaB signal transduction / 酸化的リン酸化 / cellular response to glucocorticoid stimulus / 細胞呼吸 / response to copper ion / positive regulation of mitochondrial membrane potential / response to glucagon / response to hydroperoxide / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / iron-sulfur cluster assembly / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial ribosome / respiratory chain complex I / midbrain development / hypothalamus development / adult behavior / dopamine metabolic process / mitochondrial translation / NADH dehydrogenase activity / ubiquinone binding / response to cobalamin / NADH:ユビキノン還元酵素 (水素イオン輸送型) / positive regulation of ATP biosynthetic process / acyl binding / mitochondrial ATP synthesis coupled electron transport / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / neuron development / response to hyperoxia / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / animal organ regeneration / response to cadmium ion / enzyme regulator activity / negative regulation of intrinsic apoptotic signaling pathway / response to electrical stimulus / ATP metabolic process / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 細胞呼吸 / response to cAMP / クエン酸回路 / response to organonitrogen compound / ionotropic glutamate receptor binding / 視覚 / respiratory electron transport chain 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: 3.6 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. Crystallogr. 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_17989.map.gz | 12.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17989-v30.xml emd-17989.xml | 96.4 KB 96.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17989_fsc.xml | 21.2 KB | 表示 | FSCデータファイル |
画像 | emd_17989.png | 110 KB | ||
Filedesc metadata | emd-17989.cif.gz | 18.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17989 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17989 | HTTPS FTP |
-関連構造データ
関連構造データ | 8pw5MC 8pw6C 8pw7C 8rgpC 8rgqC 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_17989.map.gz / 形式: CCP4 / 大きさ: 55.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | composite map | ||||||||||||||||||||
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 : SC respirasome from murine liver
+超分子 #1: SC respirasome from murine liver
+分子 #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+分子 #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+分子 #3: Cytochrome b
+分子 #4: Cytochrome c1, heme protein, mitochondrial
+分子 #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+分子 #6: Cytochrome b-c1 complex subunit 7
+分子 #7: Cytochrome b-c1 complex subunit 8
+分子 #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+分子 #9: Cytochrome b-c1 complex subunit 9
+分子 #10: Cytochrome b-c1 complex subunit 10
+分子 #11: Cox7a2l protein
+分子 #12: Cytochrome c oxidase subunit 1
+分子 #13: Cytochrome c oxidase subunit 2
+分子 #14: Cytochrome c oxidase subunit 3
+分子 #15: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+分子 #16: Cytochrome c oxidase subunit 5A, mitochondrial
+分子 #17: Cytochrome c oxidase subunit 5B, mitochondrial
+分子 #18: Cytochrome c oxidase subunit 6A2, mitochondrial
+分子 #19: Cytochrome c oxidase subunit 6B1
+分子 #20: Cytochrome c oxidase subunit 6C
+分子 #21: Cytochrome c oxidase subunit 7B, mitochondrial
+分子 #22: Cytochrome c oxidase subunit 7C, mitochondrial
+分子 #23: Cytochrome c oxidase subunit 8B, mitochondrial
+分子 #24: Cytochrome c oxidase subunit 7A2, mitochondrial
+分子 #25: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+分子 #26: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+分子 #27: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+分子 #28: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #29: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #30: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+分子 #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+分子 #32: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+分子 #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+分子 #34: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #35: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #36: Acyl carrier protein, mitochondrial
+分子 #37: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+分子 #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #39: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #40: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+分子 #41: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+分子 #42: NADH-ubiquinone oxidoreductase chain 3
+分子 #43: NADH-ubiquinone oxidoreductase chain 1
+分子 #44: NADH-ubiquinone oxidoreductase chain 6
+分子 #45: NADH-ubiquinone oxidoreductase chain 4L
+分子 #46: NADH-ubiquinone oxidoreductase chain 5
+分子 #47: NADH-ubiquinone oxidoreductase chain 4
+分子 #48: NADH-ubiquinone oxidoreductase chain 2
+分子 #49: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #51: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+分子 #53: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #54: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #55: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #56: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #57: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+分子 #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+分子 #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+分子 #61: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+分子 #62: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+分子 #63: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+分子 #64: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #65: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+分子 #66: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #67: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #68: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #69: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #70: CARDIOLIPIN
+分子 #71: PROTOPORPHYRIN IX CONTAINING FE
+分子 #72: HEME C
+分子 #73: FE2/S2 (INORGANIC) CLUSTER
+分子 #74: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #75: COPPER (II) ION
+分子 #76: SODIUM ION
+分子 #77: HEME-A
+分子 #78: MAGNESIUM ION
+分子 #79: DINUCLEAR COPPER ION
+分子 #80: ZINC ION
+分子 #81: TRISTEAROYLGLYCEROL
+分子 #82: IRON/SULFUR CLUSTER
+分子 #83: FLAVIN MONONUCLEOTIDE
+分子 #84: POTASSIUM ION
+分子 #85: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #86: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+分子 #87: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
-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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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 FIELDBright-field microscopy / 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 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |