+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-4093 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Entire ovine respiratory complex I, Combined Map | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
機能・相同性 | ![]() Complex I biogenesis / Respiratory electron transport / : / oxidoreductase activity, acting on NAD(P)H / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : ...Complex I biogenesis / Respiratory electron transport / : / oxidoreductase activity, acting on NAD(P)H / 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 / ATP metabolic process / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / apoptotic signaling pathway / electron transport chain / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrial matrix / negative regulation of DNA-templated transcription / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
![]() | Fiedorczuk K / Letts JA / Sazanov LA | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() タイトル: Atomic structure of the entire mammalian mitochondrial complex I. 著者: Karol Fiedorczuk / James A Letts / Gianluca Degliesposti / Karol Kaszuba / Mark Skehel / Leonid A Sazanov / ![]() ![]() 要旨: Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation ...Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 3 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 61.3 KB 61.3 KB | 表示 表示 | ![]() |
画像 | ![]() | 88.3 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 218.2 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 217.3 KB | 表示 | |
XML形式データ | ![]() | 4.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-
試料の構成要素
+全体 : Mitochondrial complex I
+超分子 #1: Mitochondrial complex I
+分子 #1: Mitochondrial complex I, 51 kDa subunit
+分子 #2: Mitochondrial complex I, 24 kDa subunit
+分子 #3: Mitochondrial complex I, 75 kDa subunit
+分子 #4: Mitochondrial complex I, 49 kDa subunit
+分子 #5: Mitochondrial complex I, 30 kDa subunit
+分子 #6: Mitochondrial complex I, PSST subunit
+分子 #7: Mitochondrial complex I, TYKY subunit
+分子 #8: Mitochondrial complex I, ND1 subunit
+分子 #9: Mitochondrial complex I, ND2 subunit
+分子 #10: Mitochondrial complex I, ND3 subunit
+分子 #11: Mitochondrial complex I, ND4 subunit
+分子 #12: Mitochondrial complex I, ND4L subunit
+分子 #13: Mitochondrial complex I, ND5 subunit
+分子 #14: Mitochondrial complex I, ND6 subunit
+分子 #15: Mitochondrial complex I, 10 kDa subunit
+分子 #16: Mitochondrial complex I, 13 kDa subunit
+分子 #17: Mitochondrial complex I, 18 kDa subunit
+分子 #18: Mitochondrial complex I, 39 kDa subunit
+分子 #19: Mitochondrial complex I, B8 subunit
+分子 #20: Mitochondrial complex I, B13 subunit
+分子 #21: Mitochondrial complex I, B14 subunit
+分子 #22: Mitochondrial complex I, B14.5a subunit
+分子 #23: Mitochondrial complex I, B17.2 subunit
+分子 #24: Acyl carrier protein
+分子 #25: Mitochondrial complex I, 42 kDa subunit
+分子 #26: Mitochondrial complex I, 15 kDa subunit
+分子 #27: Mitochondrial complex I, B9 subunit
+分子 #28: Mitochondrial complex I, B12 subunit
+分子 #29: Mitochondrial complex I, B14.5b subunit
+分子 #30: Mitochondrial complex I, B15 subunit
+分子 #31: Mitochondrial complex I, B16.6 subunit
+分子 #32: Mitochondrial complex I, B17 subunit
+分子 #33: Mitochondrial complex I, B18 subunit
+分子 #34: Mitochondrial complex I, B22 subunit
+分子 #35: Mitochondrial complex I, AGGG subunit
+分子 #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+分子 #37: Mitochondrial complex I, ESSS subunit
+分子 #38: Mitochondrial complex I, KFYI subunit
+分子 #39: Mitochondrial complex I, MNLL subunit
+分子 #40: Mitochondrial complex I, MWFE subunit
+分子 #41: Mitochondrial complex I, PDSW subunit
+分子 #42: Mitochondrial complex I, PGIV subunit
+分子 #43: Mitochondrial complex I, SGDH subunit
+分子 #44: Mitochondrial complex I, B14.7 subunit
+分子 #45: IRON/SULFUR CLUSTER
+分子 #46: FLAVIN MONONUCLEOTIDE
+分子 #47: FE2/S2 (INORGANIC) CLUSTER
+分子 #48: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+分子 #49: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+分子 #50: CARDIOLIPIN
+分子 #51: ZINC ION
+分子 #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+分子 #53: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+分子 #54: 4'-PHOSPHOPANTETHEINE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
濃度 | 5 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
緩衝液 | pH: 7.4 構成要素:
| ||||||||||||||||||
グリッド | モデル: Quantifoil R0.6/1 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR | ||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: 34s blotting. |
-
電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / デジタル化 - サンプリング間隔: 14.0 µm / デジタル化 - 画像ごとのフレーム数: 1-7 / 撮影したグリッド数: 2 / 実像数: 2600 / 平均露光時間: 1.0 sec. / 平均電子線量: 26.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 100720 / 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): 3.5 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
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
初期モデル | PDB ID: 詳細: For the fourteen core subunits we used as a starting point our previous structure from T. thermophilus (PDB 4HEA) with sequence adjusted to ovine and side-chains rebuilt in SQWRL4. These are ...詳細: For the fourteen core subunits we used as a starting point our previous structure from T. thermophilus (PDB 4HEA) with sequence adjusted to ovine and side-chains rebuilt in SQWRL4. These are chains 1, 2, 3, 4, 5, 6, 9, H, A, J, K, N, M and L (with the same chain IDs as in 4HEA). For the remaining supernumerary subunits it was mostly de novo building with some help from homology modeling, which in most cases was not very useful due to low sequence homology. In few cases models produced by Phyre2 server were useful and were used as a starting point, due to the presence of templates with high coverage and confidence: 42kDa (chain k) - PDB ID 1P6X (xray) 39kDa (chain d) - PDB ID 3WJ7 (xray) SDAPs (chains j and X) - PDB ID 2DNW (NMR) B8 (chain e) - PDB ID 1S3A (NMR) |
---|---|
精密化 | 空間: REAL / プロトコル: AB INITIO MODEL |
得られたモデル | ![]() PDB-5lnk: |