+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8pw7 | |||||||||
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タイトル | A respirasome from murine liver | |||||||||
要素 |
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キーワード | MEMBRANE PROTEIN / Respiratory chain super complex / mammalian mitochondria | |||||||||
機能・相同性 | 機能・相同性情報 Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis ...Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / 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 / cerebellar Purkinje cell layer development / RHOG GTPase cycle / respiratory chain complex III / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / respiratory chain complex IV assembly / pyramidal neuron development / response to mercury ion / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory system process / respiratory chain complex IV / psychomotor behavior / Mitochondrial protein degradation / regulation of oxidative phosphorylation / response to light intensity / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone-6 biosynthetic process / mitochondrial large ribosomal subunit binding / : / gliogenesis / : / response to alkaloid / neural precursor cell proliferation / oxidative phosphorylation / cytochrome-c oxidase / cardiac muscle tissue development / : / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase / adult walking behavior / oxygen sensor activity / response to copper ion / response to glucagon / cellular response to glucocorticoid stimulus / ubiquinol-cytochrome-c reductase activity / response to hydroperoxide / positive regulation of mitochondrial membrane potential / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / adult behavior / mitochondrial translation / positive regulation of ATP biosynthetic process / response to cobalamin / 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 / response to hyperoxia / cellular response to interferon-beta / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / neuron development / animal organ regeneration / quinone binding / response to cadmium ion / enzyme regulator activity / ATP synthesis coupled electron transport / response to electrical stimulus / 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 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
データ登録者 | Vercellino, I. / Sazanov, L.A. | |||||||||
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, P.V. / Adams, P.D. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8pw7.cif.gz | 2.9 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8pw7.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8pw7.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8pw7_validation.pdf.gz | 4.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8pw7_full_validation.pdf.gz | 4.3 MB | 表示 | |
XML形式データ | 8pw7_validation.xml.gz | 339.3 KB | 表示 | |
CIF形式データ | 8pw7_validation.cif.gz | 521.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pw/8pw7 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/8pw7 | HTTPS FTP |
-関連構造データ
関連構造データ | 17991MC 8pw5C 8pw6C 8rgpC 8rgqC 8rgrC 8rgtC M: このデータのモデリングに利用したマップデータ 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
-集合体
登録構造単位 |
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1 |
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-要素
+Cytochrome c oxidase subunit ... , 13種, 13分子 nopqrstuvxywz
+Cytochrome b-c1 complex subunit ... , 8種, 17分子 ALBMEPTFQGRHSJUKV
+タンパク質 , 4種, 7分子 CNDO3T1U1
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7種, 7分子 6C1D19Q17e1
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3種, 3分子 21s1
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12種, 12分子 P1S1V1W1q1r1O1X1Y1Z1a1b1
+NADH-ubiquinone oxidoreductase chain ... , 7種, 7分子 A1H1J1K1L1M1N1
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2種, 2分子 c1d1
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11種, 11分子 f1g1h1i1j1k1l1m1n1o1p1
+非ポリマー , 19種, 90分子
+詳細
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: A respirasome from murine liver / タイプ: COMPLEX / Entity ID: #1-#67 / 由来: NATURAL | ||||||||||||||||||||
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分子量 | 値: 1.7 MDa / 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: Mus musculus (ハツカネズミ) / 株: CD1 / 器官: liver / Organelle: mitochondria | ||||||||||||||||||||
緩衝液 | pH: 7.7 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R0.6/1 | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277.15 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm / Calibrated defocus min: 500 nm / 最大 デフォーカス(補正後): 2500 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 4.4 sec. / 電子線照射量: 80 e/Å2 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 |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.19_4092: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1758187 | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 57506 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 詳細: initial fitting done in chimera | ||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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拘束条件 |
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