+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30675 | |||||||||
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タイトル | Activity optimized supercomplex state3 | |||||||||
マップデータ | ||||||||||
試料 |
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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 / deoxynucleoside kinase activity / cellular respiration / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / Neutrophil degranulation / cytochrome-c oxidase activity / mitochondrial ribosome / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial translation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / 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 / ATP metabolic process / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / regulation of mitochondrial membrane potential / central nervous system development / fatty acid binding / mitochondrial membrane / apoptotic signaling pathway / electron transport chain / regulation of protein phosphorylation / mitochondrial intermembrane space / brain development / negative regulation of cell growth / 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 / 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 / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Bos taurus (ウシ) / Bovine (ウシ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.8 Å | |||||||||
データ登録者 | Jeon TJ / Lee SG / Yoo SH / Ryu JH / Kim DS / Hyun JK / Kim HM / Ryu SE | |||||||||
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
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_30675.map.gz | 12 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30675-v30.xml emd-30675.xml | 79.6 KB 79.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_30675.png | 98.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30675 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30675 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30675_validation.pdf.gz | 340.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30675_full_validation.pdf.gz | 340.2 KB | 表示 | |
XML形式データ | emd_30675_validation.xml.gz | 6.3 KB | 表示 | |
CIF形式データ | emd_30675_validation.cif.gz | 7.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30675 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30675 | HTTPS FTP |
-関連構造データ
-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_30675.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.3973 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
-試料の構成要素
+全体 : supercomplex of electron transport chain complexes
+超分子 #1: supercomplex of electron transport chain complexes
+分子 #1: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #2: NADH-ubiquinone oxidoreductase chain 6
+分子 #3: NADH-ubiquinone oxidoreductase chain 5
+分子 #4: NADH-ubiquinone oxidoreductase chain 2
+分子 #5: NADH-ubiquinone oxidoreductase chain 4
+分子 #6: NADH-ubiquinone oxidoreductase chain 4L
+分子 #7: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #8: NADH-ubiquinone oxidoreductase chain 1
+分子 #9: NADH-ubiquinone oxidoreductase chain 3
+分子 #10: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+分子 #11: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+分子 #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+分子 #13: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+分子 #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+分子 #15: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+分子 #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+分子 #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+分子 #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+分子 #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+分子 #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+分子 #31: Acyl carrier protein, mitochondrial
+分子 #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+分子 #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+分子 #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+分子 #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+分子 #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+分子 #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+分子 #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+分子 #41: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+分子 #42: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #45: Cytochrome b-c1 complex subunit 1, mitochondrial
+分子 #46: Cytochrome b-c1 complex subunit 2, mitochondrial
+分子 #47: Cytochrome b
+分子 #48: Cytochrome c1, heme protein, mitochondrial
+分子 #49: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+分子 #50: Cytochrome b-c1 complex subunit 7
+分子 #51: Cytochrome b-c1 complex subunit 8
+分子 #52: Cytochrome b-c1 complex subunit 6, mitochondrial
+分子 #53: Cytochrome b-c1 complex subunit 10
+分子 #54: Cytochrome b-c1 complex subunit 9
+分子 #55: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+分子 #56: Cytochrome c oxidase subunit 1
+分子 #57: Cytochrome c oxidase subunit 2
+分子 #58: Cytochrome c oxidase subunit 3
+分子 #59: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+分子 #60: Cytochrome c oxidase subunit 5A, mitochondrial
+分子 #61: Cytochrome c oxidase subunit 5B, mitochondrial
+分子 #62: Cytochrome c oxidase subunit 6A2, mitochondrial
+分子 #63: Cytochrome c oxidase subunit 6B1
+分子 #64: Cytochrome c oxidase subunit 6C
+分子 #65: Cytochrome c oxidase subunit 7A1, mitochondrial
+分子 #66: Cytochrome c oxidase subunit 7B, mitochondrial
+分子 #67: Cytochrome c oxidase subunit 7C, mitochondrial
+分子 #68: Cytochrome c oxidase subunit 8B, mitochondrial
+分子 #69: FE2/S2 (INORGANIC) CLUSTER
+分子 #70: CARDIOLIPIN
+分子 #71: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+分子 #72: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #73: FLAVIN MONONUCLEOTIDE
+分子 #74: IRON/SULFUR CLUSTER
+分子 #75: ZINC ION
+分子 #76: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #77: PROTOPORPHYRIN IX CONTAINING FE
+分子 #78: HEME C
+分子 #79: HEME-A
+分子 #80: COPPER (II) ION
+分子 #81: MAGNESIUM ION
-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 | tissue |
-試料調製
緩衝液 | pH: 7.4 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 400 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-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: FEI FALCON II (4k x 4k) 平均電子線量: 35.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア - 名称: CTFFIND (ver. 1.4) |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 7.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.0) / 使用した粒子像数: 24810 |
初期 角度割当 | タイプ: NOT APPLICABLE / ソフトウェア - 名称: RELION (ver. 2.0) |
最終 角度割当 | タイプ: NOT APPLICABLE / ソフトウェア - 名称: RELION (ver. 2.0) |