+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25652 | |||||||||
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Title | GATOR1-RAG-RAGULATOR - Inhibitory Complex | |||||||||
Map data | GATOR1-RAG-RAGULATOR - Inhibitory Complex | |||||||||
Sample |
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Function / homology | Function and homology information 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 / negative regulation of TOR signaling / kinase activator activity / cardiac muscle tissue development / protein localization to membrane / enzyme-substrate adaptor activity / vacuolar membrane / azurophil granule membrane / ventricular septum development / endosomal transport / negative regulation of kinase activity / Macroautophagy / regulation of cell size / lysosome organization / small GTPase-mediated signal transduction / roof of mouth development / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / RHOH GTPase cycle / CDC42 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 / specific granule membrane / positive regulation of autophagy / protein-membrane adaptor activity / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / cellular response to amino acid starvation / RAC1 GTPase cycle / cellular response to starvation / GTPase activator activity / viral genome replication / negative regulation of autophagy / guanyl-nucleotide exchange factor activity / RNA splicing / Regulation of PTEN gene transcription / cholesterol homeostasis / regulation of cell growth / positive regulation of interleukin-8 production / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / lysosome / molecular adaptor activity / endosome membrane / intracellular signal transduction / membrane raft / protein heterodimerization activity / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Egri SB / Shen K | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Cryo-EM structures of the human GATOR1-Rag-Ragulator complex reveal a spatial-constraint regulated GAP mechanism. Authors: Shawn B Egri / Christna Ouch / Hui-Ting Chou / Zhiheng Yu / Kangkang Song / Chen Xu / Kuang Shen / Abstract: 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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25652.map.gz | 306.8 MB | EMDB map data format | |
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Header (meta data) | emd-25652-v30.xml emd-25652.xml | 21.8 KB 21.8 KB | Display Display | EMDB header |
Images | emd_25652.png | 86.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25652 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25652 | HTTPS FTP |
-Related structure data
Related structure data | 7t3aMC 7t3bC 7t3cC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25652.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | GATOR1-RAG-RAGULATOR - Inhibitory Complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.655 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : GATOR1-RAG-RAGULATOR - Inhibitory Complex
+Supramolecule #1: GATOR1-RAG-RAGULATOR - Inhibitory Complex
+Macromolecule #1: GATOR complex protein DEPDC5
+Macromolecule #2: GATOR complex protein NPRL2
+Macromolecule #3: GATOR complex protein NPRL3
+Macromolecule #4: Ras-related GTP-binding protein A
+Macromolecule #5: Ras-related GTP-binding protein C
+Macromolecule #6: Ragulator complex protein LAMTOR1
+Macromolecule #7: Ragulator complex protein LAMTOR2
+Macromolecule #8: Ragulator complex protein LAMTOR3
+Macromolecule #9: Ragulator complex protein LAMTOR4
+Macromolecule #10: Ragulator complex protein LAMTOR5
+Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.0 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.3 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: NOT APPLICABLE |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 251583 |