+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7dkf | ||||||
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タイトル | Activity optimized supercomplex state4 | ||||||
要素 |
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キーワード | OXIDOREDUCTASE / respiratory / electron transport | ||||||
機能・相同性 | 機能・相同性情報 Complex I biogenesis / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / cellular response to oxygen levels / : ...Complex I biogenesis / Mitochondrial protein import / TP53 Regulates Metabolic Genes / RHOG GTPase cycle / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / mitochondrial respirasome assembly / respiratory chain complex IV / cellular response to oxygen levels / : / mitochondrial large ribosomal subunit binding / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / : / neural precursor cell proliferation / cytochrome-c oxidase / : / [2Fe-2S] cluster assembly / oxidative phosphorylation / oxygen sensor activity / quinol-cytochrome-c reductase / ubiquinone-6 biosynthetic process / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / Neutrophil degranulation / cytochrome-c oxidase activity / NADH dehydrogenase activity / mitochondrial ribosome / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial translation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / neurogenesis / : / enzyme regulator activity / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / response to cAMP / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / central nervous system development / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / structural constituent of ribosome / mitochondrial matrix / 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: 8.3 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 | 7dkf.cif.gz | 2.5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7dkf.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 7dkf.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 | 7dkf_validation.pdf.gz | 2.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7dkf_full_validation.pdf.gz | 3 MB | 表示 | |
XML形式データ | 7dkf_validation.xml.gz | 406.7 KB | 表示 | |
CIF形式データ | 7dkf_validation.cif.gz | 604.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkf ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkf | HTTPS FTP |
-関連構造データ
関連構造データ | 30706MC 7dgqC 7dgrC 7dgsC 7dgzC 7dh0C 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 b-c1 complex subunit ... , 9種, 18分子 A1M1B1N1E1Q1F1R1G1S1H1T1I1U1J1V1K1W1
+タンパク質 , 4種, 7分子 C1O1D1P1A2W2M2
+NADH-ubiquinone oxidoreductase chain ... , 7種, 7分子 22324252721262
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3種, 3分子 8292F2
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7種, 7分子 B2C2D2E2G2H2I2
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12種, 12分子 J2K2L2N2O2P2Q2R2S2T2U2V2
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11種, 11分子 X2Y2Z2a2b2c2d2f2h2g2e2
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2種, 2分子 i2j2
+Cytochrome c oxidase subunit ... , 13種, 13分子 A3B3C3D3E3F3G3H3I3J3K3L3M3
+非ポリマー , 13種, 31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: supercomplex of electron transport chain complexes / 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 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 277 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 |
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
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||
3次元再構成 | 解像度: 8.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 11651 / 対称性のタイプ: POINT |