+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jbz | ||||||
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タイトル | Crystal structure of mTOR docked into EM map of dimeric ATM kinase | ||||||
要素 | Serine/threonine-protein kinase mTOR | ||||||
キーワード | TRANSFERASE / mTOR / PIKK | ||||||
機能・相同性 | 機能・相同性情報 RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TORC2 complex / TFIIIC-class transcription factor complex binding ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / TORC2 complex / TFIIIC-class transcription factor complex binding / regulation of membrane permeability / negative regulation of lysosome organization / heart valve morphogenesis / nucleus localization / 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 / cellular response to methionine / TORC1 signaling / regulation of osteoclast differentiation / voluntary musculoskeletal movement / positive regulation of keratinocyte migration / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / ruffle organization / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / HSF1-dependent transactivation / neuronal action potential / TOR signaling / response to amino acid / regulation of macroautophagy / cellular response to nutrient levels / positive regulation of translational initiation / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / phagocytic vesicle / heart morphogenesis / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / cardiac muscle contraction / regulation of cellular response to heat / cytoskeleton organization / positive regulation of stress fiber assembly / phosphorylation / T cell costimulation / positive regulation of glycolytic process / cellular response to amino acid starvation / negative regulation of autophagy / cellular response to starvation / response to nutrient levels / response to nutrient / post-embryonic development / VEGFR2 mediated vascular permeability / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription / positive regulation of translation / regulation of cell growth / regulation of actin cytoskeleton organization / TP53 Regulates Metabolic Genes / macroautophagy / phosphoprotein binding / cellular response to amino acid stimulus / protein destabilization / protein catabolic process / multicellular organism growth / regulation of circadian rhythm / PML body / cellular response to insulin stimulus / positive regulation of peptidyl-tyrosine phosphorylation / Regulation of TP53 Degradation / rhythmic process / PIP3 activates AKT signaling 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 28 Å | ||||||
データ登録者 | Lau, W.C.Y. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3jbz.cif.gz | 212.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3jbz.ent.gz | 160.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3jbz.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 3jbz_validation.pdf.gz | 766.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3jbz_full_validation.pdf.gz | 787.8 KB | 表示 | |
XML形式データ | 3jbz_validation.xml.gz | 31.2 KB | 表示 | |
CIF形式データ | 3jbz_validation.cif.gz | 47.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbz ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbz | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 133753.281 Da / 分子数: 1 断片: C-terminal domain (UNP RESIDUES 1385-2020, 2119-2549) 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FRAP, FRAP1, FRAP2, MTOR, RAFT1, RAPT1 / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P42345, non-specific serine/threonine protein kinase | ||
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#2: 化合物 | ChemComp-ADP / | ||
#3: 化合物 | #4: 化合物 | ChemComp-MGF / | |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: dimeric ATM kinase / タイプ: COMPLEX |
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分子量 | 値: 0.7 MDa / 実験値: NO |
緩衝液 | 名称: 25 mM Tris pH 8.0, 100 mM NaCl, 1 mM TCEP, 10% glycerol pH: 8 / 詳細: 25 mM Tris, 100 mM NaCl, 1 mM TCEP, 10% glycerol |
試料 | 濃度: 0.02 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO |
染色 | タイプ: NEGATIVE / 詳細: 2% uranyl acetate / 染色剤: uranyl acetate |
試料支持 | 詳細: continuous carbon grid |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 2010 / 日付: 2015年9月1日 |
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電子銃 | 電子線源: LAB6 / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2 mm |
試料ホルダ | 温度: 293 K |
撮影 | 電子線照射量: 25 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 実像数: 251 |
画像スキャン | デジタル画像の数: 251 |
-解析
EMソフトウェア |
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対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||
3次元再構成 | 解像度: 28 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | PDB-ID: 4JSV Accession code: 4JSV / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
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