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基本情報
登録情報 | データベース: PDB / ID: 7ux2 | ||||||
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タイトル | cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex | ||||||
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![]() | SIGNALING PROTEIN / mTORC1 / TFEB / Lysosome biogenesis / Autophagy | ||||||
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 / antibacterial innate immune response / 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 / humoral immune response / 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 / embryonic placenta development / RAC3 GTPase cycle / response to amino acid / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of autophagy / specific granule membrane / positive regulation of lipid biosynthetic process / protein-membrane adaptor activity / 14-3-3 protein binding / positive regulation of TORC1 signaling / positive regulation of endothelial cell proliferation / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / cellular response to amino acid starvation / positive regulation of glycolytic process / cellular response to starvation / 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 / autophagy / cytoplasmic stress granule / positive regulation of protein localization to nucleus / GDP binding / sequence-specific double-stranded DNA binding / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / positive regulation of peptidyl-serine phosphorylation / glucose homeostasis 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: 2.9 Å | ||||||
![]() | Cui, Z. / Hurley, J. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. 著者: Zhicheng Cui / Gennaro Napolitano / Mariana E G de Araujo / Alessandra Esposito / Jlenia Monfregola / Lukas A Huber / Andrea Ballabio / James H Hurley / ![]() ![]() ![]() 要旨: The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its ...The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its mTORC1 substrate recruitment mechanism, which is strictly dependent on the amino acid-mediated activation of the RagC GTPase activating protein FLCN. TFEB lacks the TOR signalling motif responsible for the recruitment of other mTORC1 substrates. We used cryogenic-electron microscopy to determine the structure of TFEB as presented to mTORC1 for phosphorylation, which we refer to as the 'megacomplex'. Two full Rag-Ragulator complexes present each molecule of TFEB to the mTOR active site. One Rag-Ragulator complex is bound to Raptor in the canonical mode seen previously in the absence of TFEB. A second Rag-Ragulator complex (non-canonical) docks onto the first through a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB with a RagC-dependent aspartate clamp in the cleft between the Rag G domains. In cellulo mutation of the clamp drives TFEB constitutively into the nucleus while having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. The double use of RagC GDP contacts in both Rag dimers explains the strong dependence of TFEB phosphorylation on FLCN and the RagC GDP state. | ||||||
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構造の表示
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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PDBx/mmCIF形式 | ![]() | 1.1 MB | 表示 | ![]() |
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PDB形式 | ![]() | 940.3 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 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 86.7 KB | 表示 | |
CIF形式データ | ![]() | 133.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 26846MC ![]() 7uxcC ![]() 7uxhC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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 , 2種, 2分子 AP
#1: 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) ![]() ![]() |
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#9: タンパク質 | 分子量: 52926.621 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P19484 |
-Ras-related GTP-binding protein ... , 2種, 4分子 BICJ
#2: タンパク質 | 分子量: 36600.195 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 参照: UniProt: Q7L523, 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 #3: タンパク質 | 分子量: 44298.859 Da / 分子数: 2 / Mutation: S75N / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
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-Ragulator complex protein ... , 5種, 10分子 DKELFMGNHO
#4: タンパク質 | 分子量: 17762.775 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q6IAA8 #5: タンパク質 | 分子量: 13517.450 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9Y2Q5 #6: タンパク質 | 分子量: 13637.678 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9UHA4 #7: タンパク質 | 分子量: 10753.236 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q0VGL1 #8: タンパク質 | 分子量: 9622.900 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: O43504 |
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-非ポリマー , 3種, 6分子 ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
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![](data/chem/img/GDP.gif)
#10: 化合物 | #11: 化合物 | #12: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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: The Raptor-TFEB-Rag-Ragulator complex / タイプ: COMPLEX / Entity ID: #1-#9 / 由来: MULTIPLE SOURCES |
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緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: C-flat-2/1 |
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 / 最大 デフォーカス(公称値): 2200 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
ソフトウェア |
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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 | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 377569 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL / 空間: REAL | ||||||||||||||||||||||||
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: 34.77 Å2 | ||||||||||||||||||||||||
拘束条件 |
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