+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ugr | ||||||
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タイトル | In-situ structure of typeX supercomplex in respiratory chain (composite) | ||||||
要素 |
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キーワード | ELECTRON TRANSPORT / in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein | ||||||
機能・相同性 | 機能・相同性情報 Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / mitochondrial respiratory chain complex IV ...Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Mitochondrial protein degradation / mitochondrial respiratory chain complex III / cytochrome-c oxidase / cardiac muscle tissue development / mitochondrial respirasome / quinol-cytochrome-c reductase / deoxynucleoside kinase activity / cellular respiration / ubiquinol-cytochrome-c reductase activity / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vasoconstriction / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / central nervous system development / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial intermembrane space / negative regulation of cell growth / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / electron transfer activity / nuclear body / mitochondrial matrix / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Sus scrofa (ブタ) | ||||||
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: 6.5 Å | ||||||
データ登録者 | Zheng, W. / Zhang, K. / Zhu, J. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: High-resolution in situ structures of mammalian respiratory supercomplexes. 著者: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang / 要旨: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context. | ||||||
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 | 8ugr.cif.gz | 5.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ugr.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8ugr.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 | 8ugr_validation.pdf.gz | 7.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8ugr_full_validation.pdf.gz | 7.8 MB | 表示 | |
XML形式データ | 8ugr_validation.xml.gz | 697.1 KB | 表示 | |
CIF形式データ | 8ugr_validation.cif.gz | 1 MB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ugr ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ugr | HTTPS FTP |
-関連構造データ
関連構造データ | 42233MC 8ud1C 8ueoC 8uepC 8ueqC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 8ugfC 8uggC 8ughC 8ugiC 8ugjC 8ugkC 8uglC 8ugnC 8ugpC 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-ubiquinone oxidoreductase chain ... , 7種, 14分子 1A5A1H5H1J5J1K5K1L5L1M5M1N5N
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7種, 14分子 1B5B1C5C1D5D1I5I1Q5Q1R5R1e5e
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3種, 6分子 1E5E1F5F1s5s
+タンパク質 , 4種, 14分子 1G5G3C3P6C6P3D3Q6D6Q3J3W6J6W
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10種, 20分子 1O5O1S5S1V5V1W5W1X5X1Y5Y1a5a1b5b1q5q1r5r
+NADH:ubiquinone oxidoreductase subunit ... , 4種, 10分子 1P5P1T1U5T5U1Z5Z1j5j
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2種, 4分子 1c5c1d5d
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10種, 20分子 1f5f1g5g1h5h1i5i1k5k1l5l1m5m1n5n1o5o1p5p
+Cytochrome b-c1 complex subunit ... , 7種, 32分子 3A3N6A6N3B3O6B6O3E3I3R3V6E6I6R6V3F3S6F6S3G3T6G6T3H3U6H6U3X3Y6X6Y
+Cytochrome c oxidase subunit ... , 14種, 28分子 4A8A4B8B4C8C4D8D4E8E4F8F4G8G4H8H4I8I4J8J4K8K4L8L4M8M4N8N
+非ポリマー , 25種, 190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: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria タイプ: COMPLEX / Entity ID: #1-#39, #41-#68 / 由来: NATURAL |
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由来(天然) | 生物種: Sus scrofaSus scrofa (ブタ) |
緩衝液 | pH: 7 |
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 / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1300 nm / Cs: 2.7 mm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 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 | ||||||||||||||||||||||||
3次元再構成 | 解像度: 6.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 60000 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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