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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7owg | ||||||||||||
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タイトル | human DEPTOR in a complex with mutant human mTORC1 A1459P | ||||||||||||
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![]() | SIGNALING PROTEIN / kinase / PIKK / mTOR / cancer-associated mutation / DEPTOR / partial inhibitor / cancer / PDZ / non-canonical PDZ binding | ||||||||||||
機能・相同性 | ![]() negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation ...negative regulation of TORC2 signaling / regulation of extrinsic apoptotic signaling pathway / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / regulation of membrane permeability / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC2 complex / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of autophagosome assembly / calcineurin-NFAT signaling cascade / nucleus localization / TORC1 signaling / voluntary musculoskeletal movement / positive regulation of odontoblast differentiation / 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 / phosphatidic acid binding / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cell size / ruffle organization / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / enzyme-substrate adaptor activity / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / negative regulation of TOR signaling / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of cell size / Macroautophagy / positive regulation of oligodendrocyte differentiation / negative regulation of macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / protein kinase inhibitor activity / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels / positive regulation of phosphoprotein phosphatase activity / social behavior / HSF1-dependent transactivation / positive regulation of TOR signaling / TOR signaling / neuronal action potential / positive regulation of translational initiation / response to amino acid / positive regulation of G1/S transition of mitotic cell cycle / regulation of macroautophagy / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of autophagy / positive regulation of epithelial to mesenchymal transition / positive regulation of lamellipodium assembly / positive regulation of lipid biosynthetic process / heart morphogenesis / cardiac muscle contraction / regulation of cellular response to heat / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / 14-3-3 protein binding / cytoskeleton organization / positive regulation of endothelial cell proliferation / T cell costimulation / cellular response to amino acid starvation / cellular response to starvation / phagocytic vesicle / positive regulation of glycolytic process / negative regulation of autophagy / protein serine/threonine kinase activator activity / response to nutrient levels / response to nutrient / post-embryonic development / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.7 Å | ||||||||||||
![]() | Heimhalt, M. / Berndt, A. / Wagstaff, J. / Anandapadamanaban, M. / Perisic, O. / Maslen, S. / McLaughlin, S. / Yu, W.-H. / Masson, G.R. / Boland, A. ...Heimhalt, M. / Berndt, A. / Wagstaff, J. / Anandapadamanaban, M. / Perisic, O. / Maslen, S. / McLaughlin, S. / Yu, W.-H. / Masson, G.R. / Boland, A. / Ni, X. / Yamashita, K. / Murshudov, G.N. / Skehel, M. / Freund, S.M. / Williams, R.L. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace. 著者: Maren Heimhalt / Alex Berndt / Jane Wagstaff / Madhanagopal Anandapadamanaban / Olga Perisic / Sarah Maslen / Stephen McLaughlin / Conny Wing-Heng Yu / Glenn R Masson / Andreas Boland / ...著者: Maren Heimhalt / Alex Berndt / Jane Wagstaff / Madhanagopal Anandapadamanaban / Olga Perisic / Sarah Maslen / Stephen McLaughlin / Conny Wing-Heng Yu / Glenn R Masson / Andreas Boland / Xiaodan Ni / Keitaro Yamashita / Garib N Murshudov / Mark Skehel / Stefan M Freund / Roger L Williams / ![]() ![]() 要旨: The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted ...The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition. | ||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 1.2 MB | 表示 | ![]() |
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PDB形式 | ![]() | 1 MB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 959.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 970.8 KB | 表示 | |
XML形式データ | ![]() | 89.1 KB | 表示 | |
CIF形式データ | ![]() | 131.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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非結晶学的対称性 (NCS) | NCS oper:
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要素
#1: タンパク質 | 分子量: 287570.312 Da / 分子数: 1 / 変異: A1459P / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 参照: UniProt: P42345, non-specific serine/threonine protein kinase |
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#2: タンパク質 | 分子量: 35910.090 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#3: タンパク質 | 分子量: 46365.832 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 詳細 (発現宿主): GST(tev)-Human_DEPTOR_1-409 (S204,N389 natural variant) 発現宿主: ![]() ![]() |
#4: タンパク質 | 分子量: 149200.016 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
-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 |
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試料調製
構成要素 |
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分子量 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 詳細: 50 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM TCEP, 1 mM MgCl2, 500 uM AMP-PNP | ||||||||||||||||||||||||||||
試料 | 濃度: 0.6 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Purified mutant mTORC1 A1459P and DEPTOR were preincubated in the presence of MgCl2 and AMP-PNP for 20 min and used for cryo-EM grid preparation. | ||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 287 K / 詳細: blotting time of 2 s and a force of -15. |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): -3000 nm / 最小 デフォーカス(公称値): -1400 nm / Cs: 2.7 mm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 最高温度: 100 K / 最低温度: 100 K |
撮影 | 平均露光時間: 2.5 sec. / 電子線照射量: 56 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 2 / 実像数: 4759 |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
画像スキャン | 横: 6000 / 縦: 4000 |
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解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0272 / 分類: 精密化 / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / 日付: 2020年2月9日 解説: (un)restrained refinement or idealisation of macromolecular structures | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 376784 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 500000 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 145.7 / プロトコル: FLEXIBLE FIT / 空間: RECIPROCAL / Target criteria: Correlation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6BCX PDB chain-ID: B / Pdb chain residue range: 1-2549 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | 解像度: 4.7→299.244 Å / Cor.coef. Fo:Fc: 0.974 / WRfactor Rwork: 0.342 / SU B: 108.861 / SU ML: 1.072 / Average fsc overall: 0.7062 / Average fsc work: 0.7062 / ESU R: 0.804 / 詳細: Hydrogens have been added in their riding positions
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溶媒の処理 | 溶媒モデル: BABINET MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 122.054 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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