+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-42167 | |||||||||
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タイトル | In-situ complex I with Q10 (State-beta) | |||||||||
マップデータ | In-situ complex I with Q10 intermediate-I | |||||||||
試料 |
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キーワード | in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein / electron transport | |||||||||
機能・相同性 | 機能・相同性情報 RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / oxidoreductase activity, acting on NAD(P)H / cardiac muscle tissue development / cellular respiration / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / oxidoreductase activity, acting on NAD(P)H / cardiac muscle tissue development / cellular respiration / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / respiratory chain complex I / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / negative regulation of intrinsic apoptotic signaling pathway / ATP synthesis coupled electron transport / quinone binding / : / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / regulation of protein phosphorylation / brain development / negative regulation of cell growth / mitochondrial intermembrane space / 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 / nuclear body / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Sus scrofa (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
データ登録者 | Zheng W / Zhu J / Zhang K | |||||||||
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
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_42167.map.gz | 62.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-42167-v30.xml emd-42167.xml | 65.1 KB 65.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_42167.png | 74.3 KB | ||
Filedesc metadata | emd-42167.cif.gz | 14.2 KB | ||
その他 | emd_42167_half_map_1.map.gz emd_42167_half_map_2.map.gz | 116 MB 116 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-42167 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42167 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_42167_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_42167_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_42167_validation.xml.gz | 13.6 KB | 表示 | |
CIF形式データ | emd_42167_validation.cif.gz | 16.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42167 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42167 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ueqMC 8ud1C 8ueoC 8uepC 8uerC 8uesC 8uetC 8ueuC 8uevC 8uewC 8uexC 8ueyC 8uezC 8ugdC 8ugeC 8ugfC 8uggC 8ughC 8ugiC 8ugjC 8ugkC 8uglC 8ugnC 8ugpC 8ugrC M: このマップから作成された原子モデル 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
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_42167.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | In-situ complex I with Q10 intermediate-I | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.39 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
-ハーフマップ: In-situ complex I with Q10 intermediate-I
ファイル | emd_42167_half_map_1.map | ||||||||||||
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注釈 | In-situ complex I with Q10 intermediate-I | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: In-situ complex I with Q10 intermediate-I
ファイル | emd_42167_half_map_2.map | ||||||||||||
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注釈 | In-situ complex I with Q10 intermediate-I | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : In-situ cryo-EM structure of respiratory supercomplex by directly...
+超分子 #1: In-situ cryo-EM structure of respiratory supercomplex by directly...
+分子 #1: NADH-ubiquinone oxidoreductase chain 3
+分子 #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+分子 #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+分子 #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+分子 #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+分子 #8: NADH-ubiquinone oxidoreductase chain 1
+分子 #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+分子 #10: NADH-ubiquinone oxidoreductase chain 6
+分子 #11: NADH-ubiquinone oxidoreductase chain 4L
+分子 #12: NADH-ubiquinone oxidoreductase chain 5
+分子 #13: NADH-ubiquinone oxidoreductase chain 4
+分子 #14: NADH-ubiquinone oxidoreductase chain 2
+分子 #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #16: NADH:ubiquinone oxidoreductase subunit A9
+分子 #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+分子 #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #20: NADH:ubiquinone oxidoreductase subunit AB1
+分子 #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isof...
+分子 #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #25: NADH:ubiquinone oxidoreductase subunit A13
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus ...
+分子 #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+分子 #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+分子 #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+分子 #35: NADH:ubiquinone oxidoreductase subunit B2
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+分子 #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+分子 #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+分子 #45: IRON/SULFUR CLUSTER
+分子 #46: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #47: UBIQUINONE-10
+分子 #48: FE2/S2 (INORGANIC) CLUSTER
+分子 #49: FLAVIN MONONUCLEOTIDE
+分子 #50: POTASSIUM ION
+分子 #51: MYRISTIC ACID
+分子 #52: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #53: CARDIOLIPIN
+分子 #54: GUANOSINE-5'-TRIPHOSPHATE
+分子 #55: MAGNESIUM ION
+分子 #56: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #57: ZINC ION
+分子 #58: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
-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
緩衝液 | pH: 7 |
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凍結 | 凍結剤: ETHANE |
-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) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 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): 3.0 µm / 最小 デフォーカス(公称値): 1.3 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 29000 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |