+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26861 | |||||||||
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タイトル | A composite cryo-EM map of the mTORC1-TFEB-Rag-Ragulator complex | |||||||||
マップデータ | A composite map of the symmetric mTORC1-Rag-Ragulator complex | |||||||||
試料 |
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キーワード | mTORC1 / TFEB / Lysosome biogenesis / Autophagy / SIGNALING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 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 / positive regulation of cytoplasmic translational initiation / protein localization to cell junction ...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 / positive regulation of cytoplasmic translational initiation / protein localization to cell junction / 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 / antibacterial innate immune response / positive regulation of wound healing, spreading of epidermal cells / cellular response to leucine starvation / regulation of TORC1 signaling / regulation of membrane permeability / TFIIIC-class transcription factor complex binding / heart valve morphogenesis / 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 / protein localization to lysosome / 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 / regulation of TOR signaling / endosome organization / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / cellular response to nutrient / lysosome localization / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cell size / ruffle organization / 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 / 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 / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / negative regulation of macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / RHOJ GTPase cycle / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / RHOQ GTPase cycle / 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 / 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 / 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 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | |||||||||
データ登録者 | Cui Z / Hurley J | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2023 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. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_26861.map.gz | 700.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-26861-v30.xml emd-26861.xml | 27.7 KB 27.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_26861.png | 92.2 KB | ||
Filedesc metadata | emd-26861.cif.gz | 9.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26861 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_26861_validation.pdf.gz | 534.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_26861_full_validation.pdf.gz | 534.3 KB | 表示 | |
XML形式データ | emd_26861_validation.xml.gz | 8.8 KB | 表示 | |
CIF形式データ | emd_26861_validation.cif.gz | 10.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26861 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26861 | HTTPS FTP |
-関連構造データ
関連構造データ | 7uxhMC 7ux2C 7uxcC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_26861.map.gz / 形式: CCP4 / 大きさ: 775.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | A composite map of the symmetric mTORC1-Rag-Ragulator complex | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
+全体 : The mTORC1-TFEB-Rag-Ragulator complex
+超分子 #1: The mTORC1-TFEB-Rag-Ragulator complex
+分子 #1: Serine/threonine-protein kinase mTOR
+分子 #2: Target of rapamycin complex subunit LST8
+分子 #3: Regulatory-associated protein of mTOR
+分子 #4: Ras-related GTP-binding protein A
+分子 #5: Ras-related GTP-binding protein C
+分子 #6: Ragulator complex protein LAMTOR1
+分子 #7: Ragulator complex protein LAMTOR2
+分子 #8: Ragulator complex protein LAMTOR3
+分子 #9: Ragulator complex protein LAMTOR4
+分子 #10: Ragulator complex protein LAMTOR5
+分子 #11: Transcription factor EB
+分子 #12: INOSITOL HEXAKISPHOSPHATE
+分子 #13: GUANOSINE-5'-TRIPHOSPHATE
+分子 #14: MAGNESIUM ION
+分子 #15: GUANOSINE-5'-DIPHOSPHATE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL / In silico モデル: ab-initio reconstruction by cryoSPARC |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC (ver. 3.2) / 使用した粒子像数: 192332 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |