+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6501 | |||||||||
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タイトル | Electron microscopy of dimeric ATM kinase | |||||||||
マップデータ | Reconstruction of dimeric ATM kinase | |||||||||
試料 |
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キーワード | ATM kinase / DNA damage (DNA修復) / Electron microscopy (電子顕微鏡) | |||||||||
機能・相同性 | 機能・相同性情報 RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex ...RNA polymerase III type 2 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of pentose-phosphate shunt / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / heart valve morphogenesis / regulation of membrane permeability / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / regulation of autophagosome assembly / TORC1 signaling / voluntary musculoskeletal movement / regulation of osteoclast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / cellular response to nutrient / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / nucleus localization / ruffle organization / negative regulation of cell size / cellular response to osmotic stress / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of protein localization to nucleus / regulation of myelination / negative regulation of calcineurin-NFAT signaling cascade / オートファジー / regulation of cell size / negative regulation of macroautophagy / lysosome organization / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / positive regulation of myotube differentiation / behavioral response to pain / MTOR / oligodendrocyte differentiation / mTORC1-mediated signalling / germ cell development / Constitutive Signaling by AKT1 E17K in Cancer / cellular response to nutrient levels / CD28 dependent PI3K/Akt signaling / positive regulation of phosphoprotein phosphatase activity / positive regulation of translational initiation / neuronal action potential / HSF1-dependent transactivation / positive regulation of epithelial to mesenchymal transition / regulation of macroautophagy / 細胞内膜系 / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / positive regulation of lipid biosynthetic process / phagocytic vesicle / positive regulation of lamellipodium assembly / heart morphogenesis / regulation of cellular response to heat / cytoskeleton organization / cardiac muscle contraction / positive regulation of stress fiber assembly / cellular response to amino acid starvation / T cell costimulation / cellular response to starvation / positive regulation of glycolytic process / response to nutrient levels / post-embryonic development / response to nutrient / negative regulation of autophagy / positive regulation of translation / VEGFR2 mediated vascular permeability / Regulation of PTEN gene transcription / regulation of signal transduction by p53 class mediator / regulation of cell growth / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / オートファジー / phosphoprotein binding / protein catabolic process / protein destabilization / multicellular organism growth / regulation of circadian rhythm / PML body / cellular response to insulin stimulus / rhythmic process / positive regulation of peptidyl-tyrosine phosphorylation / Regulation of TP53 Degradation / ribosome binding / PIP3 activates AKT signaling / 核膜 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 28.0 Å | |||||||||
データ登録者 | Lau W / Li Y / Liu Z / Gao Y / Zhang Q / Huen MSY | |||||||||
引用 | ジャーナル: Cell Cycle / 年: 2016 タイトル: Structure of the human dimeric ATM kinase. 著者: Wilson C Y Lau / Yinyin Li / Zhe Liu / Yuanzhu Gao / Qinfen Zhang / Michael S Y Huen / 要旨: DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves ...DNA-double strand breaks activate the serine/threonine protein kinase ataxia-telangiectasia mutated (ATM) to initiate DNA damage signal transduction. This activation process involves autophosphorylation and dissociation of inert ATM dimers into monomers that are catalytically active. Using single-particle electron microscopy (EM), we determined the structure of dimeric ATM in its resting state. The EM map could accommodate the crystal structure of the N-terminal truncated mammalian target of rapamycin (mTOR), a closely related enzyme of the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family, allowing for the localization of the N- and the C-terminal regions of ATM. In the dimeric structure, the actives sites are buried, restricting the access of the substrates to these sites. The unanticipated domain organization of ATM provides a basis for understanding its mechanism of inhibition. | |||||||||
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_6501.map.gz | 642 KB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6501-v30.xml emd-6501.xml | 10 KB 10 KB | 表示 表示 | EMDBヘッダ |
画像 | 400_6501.gif 80_6501.gif | 33.3 KB 3.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6501 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6501 | 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_6501.map.gz / 形式: CCP4 / 大きさ: 3.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of dimeric ATM kinase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 4.61 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 : Dimeric ATM kinase structure
全体 | 名称: Dimeric ATM kinase structure |
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要素 |
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-超分子 #1000: Dimeric ATM kinase structure
超分子 | 名称: Dimeric ATM kinase structure / タイプ: sample / ID: 1000 / 詳細: The sample was monodisperse / 集合状態: 2 / Number unique components: 1 |
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分子量 | 理論値: 700 KDa |
-分子 #1: Dimeric ATM kinase
分子 | 名称: Dimeric ATM kinase / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 集合状態: Dimer / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human |
分子量 | 理論値: 700 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: 293T / 組換プラスミド: pcDNA-FLAG-His-ATM wt |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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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
濃度 | 0.02 mg/mL |
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緩衝液 | pH: 8 / 詳細: 25 mM Tris, 100 mM NaCl, 1 mM TCEP, 10% glycerol |
染色 | タイプ: NEGATIVE / 詳細: 2% w/v uranyl acetate |
グリッド | 詳細: continuous carbon coated copper grids |
凍結 | 凍結剤: NONE / 装置: OTHER |
-電子顕微鏡法
顕微鏡 | JEOL 2010 |
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電子線 | 加速電圧: 200 kV / 電子線源: LAB6 |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / 最大 デフォーカス(公称値): 4.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
温度 | 平均: 296 K |
日付 | 2015年7月1日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 実像数: 251 / 平均電子線量: 25 e/Å2 |
-画像解析
CTF補正 | 詳細: class average |
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最終 再構成 | アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 28.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: SIMPLE, EMAN2 / 使用した粒子像数: 3885 |