+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9534 | |||||||||
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タイトル | Architecture of mammalian respirasome | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / : / regulation of oxidative phosphorylation / Respiratory electron transport ...TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / respiratory chain complex IV / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / : / regulation of oxidative phosphorylation / Respiratory electron transport / gliogenesis / anterograde axonal transport / Mitochondrial protein degradation / : / neural precursor cell proliferation / cytochrome-c oxidase / : / oxidative phosphorylation / oxygen sensor activity / quinol-cytochrome-c reductase / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / NADH dehydrogenase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / enzyme regulator activity / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / axon cytoplasm / respiratory electron transport chain / reactive oxygen species metabolic process / : / mitochondrial electron transport, NADH to ubiquinone / central nervous system development / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Sus scrofa (ブタ) / Bovine (ウシ) / Pig (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.4 Å | |||||||||
データ登録者 | Gu J / Wu M / Guo R / Yang M | |||||||||
引用 | ジャーナル: Nature / 年: 2016 タイトル: The architecture of the mammalian respirasome. 著者: Jinke Gu / Meng Wu / Runyu Guo / Kaige Yan / Jianlin Lei / Ning Gao / Maojun Yang / 要旨: The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing ...The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_9534.map.gz | 26.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9534-v30.xml emd-9534.xml | 75.9 KB 75.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9534.png | 15.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9534 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9534 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9534_validation.pdf.gz | 328.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9534_full_validation.pdf.gz | 328.4 KB | 表示 | |
XML形式データ | emd_9534_validation.xml.gz | 7.7 KB | 表示 | |
CIF形式データ | emd_9534_validation.cif.gz | 8.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9534 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9534 | 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_9534.map.gz / 形式: CCP4 / 大きさ: 421.9 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: 1.05296 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Respirasome
+超分子 #1: Respirasome
+分子 #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+分子 #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+分子 #3: Cytochrome b
+分子 #4: Cytochrome c1, heme protein, mitochondrial
+分子 #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+分子 #6: Cytochrome b-c1 complex subunit 7
+分子 #7: Cytochrome b-c1 complex subunit 8
+分子 #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+分子 #9: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+分子 #10: Cytochrome b-c1 complex subunit 9
+分子 #11: Cytochrome b-c1 complex subunit 10
+分子 #12: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
+分子 #13: NADH-ubiquinone oxidoreductase 75 kDa subunit
+分子 #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
+分子 #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7
+分子 #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8
+分子 #17: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+分子 #18: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+分子 #19: NADH-ubiquinone oxidoreductase chain 1
+分子 #20: NADH-ubiquinone oxidoreductase chain 2
+分子 #21: NADH-ubiquinone oxidoreductase chain 3
+分子 #22: NADH-ubiquinone oxidoreductase chain 4
+分子 #23: NADH-ubiquinone oxidoreductase chain 4L
+分子 #24: NADH-ubiquinone oxidoreductase chain 5
+分子 #25: NADH-ubiquinone oxidoreductase chain 6
+分子 #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+分子 #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+分子 #28: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+分子 #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
+分子 #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+分子 #31: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+分子 #32: Acyl carrier protein
+分子 #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
+分子 #34: Mitochondrial NADH dehydrogenase Fe-S protein 4
+分子 #35: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+分子 #36: Cytochrome c oxidase subunit 3
+分子 #37: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+分子 #38: Cytochrome c oxidase subunit 5A, mitochondrial
+分子 #39: Cytochrome c oxidase subunit 5B, mitochondrial
+分子 #40: Cytochrome c oxidase subunit 6A2, mitochondrial
+分子 #41: Cytochrome c oxidase subunit 6B1
+分子 #42: Cytochrome c oxidase subunit 6C
+分子 #43: Cytochrome c oxidase subunit 7A1, mitochondrial
+分子 #44: Cytochrome c oxidase subunit 7B, mitochondrial
+分子 #45: Cytochrome c oxidase subunit 7C, mitochondrial
+分子 #46: Cytochrome c oxidase subunit 8B, mitochondrial
+分子 #47: Cytochrome c oxidase subunit 1
+分子 #48: Cytochrome c oxidase subunit 2
+分子 #49: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+分子 #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+分子 #51: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+分子 #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+分子 #53: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+分子 #54: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+分子 #55: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+分子 #56: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+分子 #57: NADH dehydrogenase [ubiquinone] 1 subunit C2
+分子 #58: NADH dehydrogenase [ubiquinone] 1 subunit C1
+分子 #59: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+分子 #60: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+分子 #61: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+分子 #62: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+分子 #63: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
+分子 #64: PROTOPORPHYRIN IX CONTAINING FE
+分子 #65: HEME C
+分子 #66: FE2/S2 (INORGANIC) CLUSTER
+分子 #67: IRON/SULFUR CLUSTER
+分子 #68: FLAVIN MONONUCLEOTIDE
+分子 #69: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #70: ZINC ION
+分子 #71: HEME-A
+分子 #72: COPPER (II) ION
+分子 #73: 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 | particle |
-試料調製
緩衝液 | pH: 7.2 |
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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: NITROGEN |
-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) 検出モード: COUNTING / 平均電子線量: 1.7 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: TUNGSTEN HAIRPIN |
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
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-5gpn: |