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基本情報
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タイトル | Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney | ||||||||||||
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![]() | e2 / 2-oxoglutarate / dehydrogenase / complex / TRANSFERASE | ||||||||||||
機能・相同性 | ![]() : / succinyl-CoA metabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / mitochondrial matrix ...: / succinyl-CoA metabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / mitochondrial matrix / mitochondrion / nucleus 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: 3.5 Å | ||||||||||||
![]() | Liu S / Xia X / Zhen J / Li ZH / Zhou ZH | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney. 著者: Shiheng Liu / Xian Xia / James Zhen / Zihang Li / Z Hong Zhou / ![]() 要旨: The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members ...The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes. | ||||||||||||
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構造の表示
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ダウンロードとリンク
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マップデータ | ![]() | 13.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 17 KB 17 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 13.5 KB | 表示 | ![]() |
画像 | ![]() | 172.5 KB | ||
マスクデータ | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
その他 | ![]() ![]() | 165.1 MB 164.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 635.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 635.2 KB | 表示 | |
XML形式データ | ![]() | 21 KB | 表示 | |
CIF形式データ | ![]() | 27.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7uolMC ![]() 7uomC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
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ボクセルのサイズ | X=Y=Z: 1.36 Å | ||||||||||||||||||||
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_26649_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_26649_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox...
全体 | 名称: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney |
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要素 |
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-超分子 #1: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox...
超分子 | 名称: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 49 KDa |
-分子 #1: Dihydrolipoyllysine-residue succinyltransferase component of 2-ox...
分子 | 名称: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial タイプ: protein_or_peptide / ID: 1 / コピー数: 24 / 光学異性体: LEVO / EC番号: dihydrolipoyllysine-residue succinyltransferase |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 49.034414 KDa |
配列 | 文字列: MLSRSRCASR AFSRSLSAFQ KGNCPLVRRS LPGISLCQGP GYPDSRKTVI NSSNIFSVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAAA P AAAAPKAE ...文字列: MLSRSRCASR AFSRSLSAFQ KGNCPLVRRS LPGISLCQGP GYPDSRKTVI NSSNIFSVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAAA P AAAAPKAE PTVSAVPPPP AAPIPTQMPP VPSPSQPLTS KPVSAVKPTA APPRAEAGAG VGLRSEHREK MNRMRQRIAQ RL KEAQNTC AMLTTFNEID MSNIQEMRAR HKDAFLKKHN LKLGFMSAFV KASAFALQEQ PVVNAVIDDA TKEVVYRDYI DIS VAVATP RGLVVPVIRN VETMNYADIE RTISELGEKA RKNELAIEDM DGGTFTISNG GVFGSLFGTP IINPPQSAIL GMHA IVDRP VVIGGKVEVR PMMYVALTYD HRLIDGREAV TFLRKIKAAV EDPRVLLLDL UniProtKB: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7 |
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グリッド | モデル: PELCO Ultrathin Carbon with Lacey Carbon / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: LACEY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 281 K / 装置: FEI VITROBOT MARK IV |
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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 K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均露光時間: 8.0 sec. / 平均電子線量: 45.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
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): 2.6 µm / 最小 デフォーカス(公称値): 1.8 µm / 倍率(公称値): 105000 |
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 |