+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19145 | |||||||||
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タイトル | Closed Complex I from murine brain | |||||||||
マップデータ | composite 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 / 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 / respiratory system process / protein insertion into mitochondrial inner membrane / 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 / NADH dehydrogenase activity / apoptotic mitochondrial changes / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / acyl binding / neuron development / 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 / extrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / tricarboxylic acid cycle / response to organonitrogen compound / 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: 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_19145.map.gz | 6.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19145-v30.xml emd-19145.xml | 67.2 KB 67.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19145_fsc.xml | 21.1 KB | 表示 | FSCデータファイル |
画像 | emd_19145.png | 100.4 KB | ||
Filedesc metadata | emd-19145.cif.gz | 14.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19145 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19145_validation.pdf.gz | 531.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19145_full_validation.pdf.gz | 531.5 KB | 表示 | |
XML形式データ | emd_19145_validation.xml.gz | 13.5 KB | 表示 | |
CIF形式データ | emd_19145_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-19145 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19145 | HTTPS FTP |
-関連構造データ
関連構造データ | 8rgpMC 8pw5C 8pw6C 8pw7C 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_19145.map.gz / 形式: CCP4 / 大きさ: 31.7 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 : Closed Complex I from murine brain
+超分子 #1: Closed Complex I from murine brain
+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: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
+分子 #49: FE2/S2 (INORGANIC) CLUSTER
+分子 #50: FLAVIN MONONUCLEOTIDE
+分子 #51: POTASSIUM ION
+分子 #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #53: ZINC ION
+分子 #54: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+分子 #55: CARDIOLIPIN
+分子 #56: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+分子 #57: 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: 10416 / 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): 2.6 µm / 最小 デフォーカス(補正後): 0.6 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 |