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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: 6u62 | |||||||||||||||||||||||||||
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タイトル | Raptor-Rag-Ragulator complex | |||||||||||||||||||||||||||
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![]() | SIGNALING PROTEIN / signaling complex / GTPase / lysosome | |||||||||||||||||||||||||||
機能・相同性 | ![]() regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / positive regulation of pentose-phosphate shunt ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / positive regulation of pentose-phosphate shunt / regulation of TORC1 signaling / TORC1 complex / protein localization to lysosome / TORC1 signaling / positive regulation of odontoblast differentiation / regulation of TOR signaling / endosome organization / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein serine/threonine kinase inhibitor activity / protein localization to membrane / kinase activator activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / enzyme-substrate adaptor activity / positive regulation of transcription by RNA polymerase III / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / small GTPase-mediated signal transduction / lysosome organization / RHOJ GTPase cycle / protein kinase activator activity / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / social behavior / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / HSF1-dependent transactivation / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / positive regulation of G1/S transition of mitotic cell cycle / specific granule membrane / positive regulation of lipid biosynthetic process / protein-membrane adaptor activity / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / cellular response to amino acid starvation / cellular response to starvation / positive regulation of glycolytic process / negative regulation of autophagy / viral genome replication / RNA splicing / guanyl-nucleotide exchange factor activity / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / regulation of autophagy / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / response to virus / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / small GTPase binding / cytoplasmic stress granule / positive regulation of protein localization to nucleus / GDP binding / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis / protein-macromolecule adaptor activity / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / positive regulation of cell growth / positive regulation of canonical NF-kappaB signal transduction 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: 3.18 Å | |||||||||||||||||||||||||||
![]() | Rogala, K.B. / Sabatini, D.M. | |||||||||||||||||||||||||||
資金援助 | ![]() ![]()
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![]() | ![]() タイトル: Structural basis for the docking of mTORC1 on the lysosomal surface. 著者: Kacper B Rogala / Xin Gu / Jibril F Kedir / Monther Abu-Remaileh / Laura F Bianchi / Alexia M S Bottino / Rikke Dueholm / Anna Niehaus / Daan Overwijn / Ange-Célia Priso Fils / Sherry X Zhou ...著者: Kacper B Rogala / Xin Gu / Jibril F Kedir / Monther Abu-Remaileh / Laura F Bianchi / Alexia M S Bottino / Rikke Dueholm / Anna Niehaus / Daan Overwijn / Ange-Célia Priso Fils / Sherry X Zhou / Daniel Leary / Nouf N Laqtom / Edward J Brignole / David M Sabatini / ![]() 要旨: The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where ...The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome. | |||||||||||||||||||||||||||
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 | ![]() | 407.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 313.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 59.5 KB | 表示 | |
CIF形式データ | ![]() | 91.2 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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要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 154915.812 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
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-Ras-related GTP-binding protein ... , 2種, 2分子 BC
#2: タンパク質 | 分子量: 36615.168 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#3: タンパク質 | 分子量: 44334.828 Da / 分子数: 1 / Mutation: S75N, T90N / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-Ragulator complex protein ... , 5種, 5分子 DEFGH
#4: タンパク質 | 分子量: 17359.230 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#5: タンパク質 | 分子量: 13517.450 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#6: タンパク質 | 分子量: 17579.781 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#7: タンパク質 | 分子量: 10776.206 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#8: タンパク質 | 分子量: 9622.900 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-非ポリマー , 3種, 3分子 ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
#9: 化合物 | ChemComp-GTP / |
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#10: 化合物 | ChemComp-MG / |
#11: 化合物 | ChemComp-GDP / |
-詳細
研究の焦点であるリガンドがあるか | Y |
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-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 | 名称: Raptor-Rag-Ragulator / タイプ: COMPLEX / Entity ID: #1-#8 / 由来: MULTIPLE SOURCES |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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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 |
撮影 | 電子線照射量: 42 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17.1_3660: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.18 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 112037 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 61.68 Å2 | ||||||||||||||||||||||||
拘束条件 |
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