+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7dgr | ||||||
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タイトル | Activity optimized supercomplex state2 | ||||||
要素 |
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キーワード | OXIDOREDUCTASE / Complex I / respiratory / electron transport | ||||||
機能・相同性 | 機能・相同性情報 Complex III assembly / Complex I biogenesis / Complex IV assembly / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex III ...Complex III assembly / Complex I biogenesis / Complex IV assembly / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex III / respiratory chain complex IV / cellular response to oxygen levels / regulation of oxidative phosphorylation / ubiquinone-6 biosynthetic process / Respiratory electron transport / : / mitochondrial large ribosomal subunit binding / gliogenesis / : / oxidative phosphorylation / cytochrome-c oxidase / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase / oxygen sensor activity / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / Neutrophil degranulation / cytochrome-c oxidase activity / respiratory chain complex I / mitochondrial ribosome / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial translation / ubiquinone binding / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / enzyme regulator activity / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / response to cAMP / aerobic respiration / neurogenesis / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / central nervous system development / fatty acid binding / apoptotic signaling pathway / mitochondrial membrane / electron transport chain / brain development / regulation of protein phosphorylation / negative regulation of cell growth / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / structural constituent of ribosome / copper ion binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Bos taurus (ウシ) | ||||||
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: 4.6 Å | ||||||
データ登録者 | Jeon, T.J. / Lee, S.G. / Yoo, S.H. / Ryu, J.H. / Kim, D.S. / Hyun, J.K. / Kim, H.M. / Ryu, S.E. | ||||||
引用 | ジャーナル: Antioxid Redox Signal / 年: 2022 タイトル: A Dynamic Substrate Pool Revealed by cryo-EM of a Lipid-Preserved Respiratory Supercomplex. 著者: Tae Jin Jeon / Seong-Gyu Lee / Suk Hyun Yoo / Myeongbin Kim / Dabin Song / Joonghyun Ryu / Hwangseo Park / Deok-Soo Kim / Jaekyung Hyun / Ho Min Kim / Seong Eon Ryu / 要旨: Mitochondrial respiratory supercomplexes mediate redox electron transfer, generating a proton gradient for ATP synthesis. To provide structural information on the function of supercomplexes in ... Mitochondrial respiratory supercomplexes mediate redox electron transfer, generating a proton gradient for ATP synthesis. To provide structural information on the function of supercomplexes in physiologically relevant conditions, we conducted cryoelectron microscopy studies with supercomplexes in a lipid-preserving state. Here, we present cryoelectron microscopy structures of bovine respiratory supercomplex IIIIIV by using a lipid-preserving sample preparation. The preparation greatly enhances the intercomplex quinone transfer activity. The structures reveal large intercomplex motions that result in different shapes and sizes of the intercomplex space between complexes I and III, forming a dynamic substrate pool. Biochemical and structural analyses indicated that intercomplex phospholipids mediate the intercomplex motions. An analysis of the different classes of focus-refined complex I showed that structural switches due to quinone reduction led to the formation of a novel channel that could transfer reduced quinones to the intercomplex substrate pool. Our results indicate potential mechanism for the facilitated electron transfer involving a dynamic substrate pool and intercomplex movement by which supercomplexes play an active role in the regulation of metabolic flux and reactive oxygen species. | ||||||
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 | 7dgr.cif.gz | 2.5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7dgr.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 7dgr.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 | 7dgr_validation.pdf.gz | 2.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7dgr_full_validation.pdf.gz | 2.5 MB | 表示 | |
XML形式データ | 7dgr_validation.xml.gz | 280.8 KB | 表示 | |
CIF形式データ | 7dgr_validation.cif.gz | 480.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/dg/7dgr ftp://data.pdbj.org/pub/pdb/validation_reports/dg/7dgr | HTTPS FTP |
-関連構造データ
関連構造データ | 30674MC 7dgqC 7dgsC 7dgzC 7dh0C 7dkfC 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
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3種, 3分子 98F
+NADH-ubiquinone oxidoreductase chain ... , 7種, 7分子 4276531
+タンパク質 , 4種, 7分子 AWMmyoz
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7種, 7分子 BCDEGHI
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12種, 12分子 JKLNOPQRSTUV
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11種, 11分子 XYZabcdfhge
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2種, 2分子 ij
+Cytochrome b-c1 complex subunit ... , 9種, 18分子 kwlxpA0qA1rA2sB3tA3uB2vB1
+Cytochrome c oxidase subunit ... , 13種, 13分子 A9C4C2A7C0A6A4A5B4C3B0C1A8
+非ポリマー , 13種, 37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: TISSUE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: NADH-UBIQUINONE OXIDOREDUCTASE / タイプ: COMPLEX / Entity ID: #1-#68 / 由来: NATURAL |
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由来(天然) | 生物種: Bos taurus (ウシ) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-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 |
撮影 | 電子線照射量: 35 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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対称性 | 点対称性: C1 (非対称) |
3次元再構成 | 解像度: 4.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 57806 / 対称性のタイプ: POINT |