+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-40566 | |||||||||
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タイトル | human liver mitochondrial Superoxide dismutase [Mn] | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | human / liver / mitochondrial / Superoxide dismutase [Mn] / OXIDOREDUCTASE | |||||||||
機能・相同性 | 機能・相同性情報 acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / response to manganese ion / cellular response to ethanol / superoxide anion generation / hydrogen peroxide biosynthetic process / intrinsic apoptotic signaling pathway in response to oxidative stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of vascular associated smooth muscle cell apoptotic process / response to zinc ion / superoxide metabolic process / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / neuron development / response to hyperoxia / response to axon injury / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to electrical stimulus / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / post-embryonic development / removal of superoxide radicals / respiratory electron transport chain / release of cytochrome c from mitochondria / liver development / regulation of mitochondrial membrane potential / response to gamma radiation / response to activity / locomotory behavior / Transcriptional activation of mitochondrial biogenesis / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / heart development / manganese ion binding / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.91 Å | |||||||||
データ登録者 | Zhang Z / Tringides M | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Mol Cell Proteomics / 年: 2023 タイトル: High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology. 著者: Zhemin Zhang / Marios L Tringides / Christopher E Morgan / Masaru Miyagi / Jason A Mears / Charles L Hoppel / Edward W Yu / 要旨: The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of ...The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level. | |||||||||
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_40566.map.gz | 32.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-40566-v30.xml emd-40566.xml | 13.2 KB 13.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_40566_fsc.xml | 9.4 KB | 表示 | FSCデータファイル |
画像 | emd_40566.png | 144.3 KB | ||
Filedesc metadata | emd-40566.cif.gz | 4.9 KB | ||
その他 | emd_40566_half_map_1.map.gz emd_40566_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-40566 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40566 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_40566_validation.pdf.gz | 796 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_40566_full_validation.pdf.gz | 795.6 KB | 表示 | |
XML形式データ | emd_40566_validation.xml.gz | 16.4 KB | 表示 | |
CIF形式データ | emd_40566_validation.cif.gz | 21.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40566 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40566 | HTTPS FTP |
-関連構造データ
関連構造データ | 8sksMC 8sgpC 8sgrC 8sgsC 8sgvC 8shsC 8sk6C 8sk8C 8skrC 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_40566.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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: 1.07 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: #1
ファイル | emd_40566_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: #2
ファイル | emd_40566_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 |
-試料の構成要素
-全体 : Superoxide dismutase [Mn]
全体 | 名称: Superoxide dismutase [Mn] |
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要素 |
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-超分子 #1: Superoxide dismutase [Mn]
超分子 | 名称: Superoxide dismutase [Mn] / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Superoxide dismutase [Mn], mitochondrial
分子 | 名称: Superoxide dismutase [Mn], mitochondrial / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO / EC番号: superoxide dismutase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 24.782119 KDa |
配列 | 文字列: MLSRAVCGTS RQLAPVLGYL GSRQKHSLPD LPYDYGALEP HINAQIMQLH HSKHHAAYVN NLNVTEEKYQ EALAKGDVTA QIALQPALK FNGGGHINHS IFWTNLSPNG GGEPKGELLE AIKRDFGSFD KFKEKLTAAS VGVQGSGWGW LGFNKERGHL Q IAACPNQD ...文字列: MLSRAVCGTS RQLAPVLGYL GSRQKHSLPD LPYDYGALEP HINAQIMQLH HSKHHAAYVN NLNVTEEKYQ EALAKGDVTA QIALQPALK FNGGGHINHS IFWTNLSPNG GGEPKGELLE AIKRDFGSFD KFKEKLTAAS VGVQGSGWGW LGFNKERGHL Q IAACPNQD PLQGTTGLIP LLGIDVWEHA YYLQYKNVRP DYLKAIWNVI NWENVTERYM ACKK UniProtKB: Superoxide dismutase [Mn], mitochondrial |
-分子 #2: MANGANESE (II) ION
分子 | 名称: MANGANESE (II) ION / タイプ: ligand / ID: 2 / コピー数: 4 / 式: MN |
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分子量 | 理論値: 54.938 Da |
-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: 7.5 |
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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: 39.5 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 / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 81000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |