+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25654 | |||||||||
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タイトル | GATOR1-RAG-RAGULATOR - Dual Complex | |||||||||
マップデータ | GATOR1-RAG-RAGULATOR - Dual Complex | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 GATOR1 complex / 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 / aorta morphogenesis ...GATOR1 complex / 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 / aorta morphogenesis / protein localization to cell junction / regulation of TORC1 signaling / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / enzyme-substrate adaptor activity / cardiac muscle tissue development / negative regulation of TOR signaling / vacuolar membrane / ventricular septum development / azurophil granule membrane / endosomal transport / negative regulation of kinase activity / regulation of cell size / Macroautophagy / small GTPase-mediated signal transduction / lysosome organization / roof of mouth development / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / positive regulation of autophagy / specific granule membrane / protein-membrane adaptor activity / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / cellular response to amino acid starvation / cellular response to starvation / negative regulation of autophagy / viral genome replication / RNA splicing / GTPase activator activity / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / phosphoprotein binding / TP53 Regulates Metabolic Genes / 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 / positive regulation of protein localization to nucleus / GDP binding / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / glucose homeostasis / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / intracellular signal transduction / membrane raft / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding 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: 4.0 Å | |||||||||
データ登録者 | Egri SB / Shen K | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism. 著者: Shawn B Egri / Christna Ouch / Hui-Ting Chou / Zhiheng Yu / Kangkang Song / Chen Xu / Kuang Shen / 要旨: mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface ...mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process. | |||||||||
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_25654.map.gz | 350.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25654-v30.xml emd-25654.xml | 23.4 KB 23.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25654.png | 101.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25654 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25654 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25654_validation.pdf.gz | 454 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25654_full_validation.pdf.gz | 453.5 KB | 表示 | |
XML形式データ | emd_25654_validation.xml.gz | 7.7 KB | 表示 | |
CIF形式データ | emd_25654_validation.cif.gz | 8.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25654 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25654 | HTTPS FTP |
-関連構造データ
-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_25654.map.gz / 形式: CCP4 / 大きさ: 371.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | GATOR1-RAG-RAGULATOR - Dual Complex | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 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 : GATOR1-RAG-RAGULATOR - Dual Complex
+超分子 #1: GATOR1-RAG-RAGULATOR - Dual Complex
+分子 #1: GATOR complex protein NPRL2
+分子 #2: GATOR complex protein DEPDC5
+分子 #3: Ragulator complex protein LAMTOR3
+分子 #4: Ragulator complex protein LAMTOR2
+分子 #5: Ragulator complex protein LAMTOR5
+分子 #6: Ragulator complex protein LAMTOR4
+分子 #7: Ragulator complex protein LAMTOR1
+分子 #8: GATOR complex protein NPRL3
+分子 #9: Ras-related GTP-binding protein A
+分子 #10: Ras-related GTP-binding protein C
+分子 #11: Ras-related GTP-binding protein C
+分子 #12: GUANOSINE-5'-DIPHOSPHATE
+分子 #13: ALUMINUM FLUORIDE
-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: 52.6 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): -3.0 µm / 最小 デフォーカス(公称値): -1.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 56117 |
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初期 角度割当 | タイプ: NOT APPLICABLE |
最終 角度割当 | タイプ: NOT APPLICABLE |