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Open data
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Basic information
Entry | Database: PDB / ID: 6ces | ||||||||||||||||||||||||
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Title | Cryo-EM structure of GATOR1-RAG | ||||||||||||||||||||||||
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![]() | SIGNALING PROTEIN / mTORC1 amino-acid sensing lysosome growth control | ||||||||||||||||||||||||
Function / homology | ![]() GATOR1 complex / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / aorta morphogenesis / regulation of TORC1 signaling / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / MTOR signalling / Amino acids regulate mTORC1 ...GATOR1 complex / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / aorta morphogenesis / regulation of TORC1 signaling / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / enzyme-substrate adaptor activity / cardiac muscle tissue development / negative regulation of TOR signaling / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / Macroautophagy / small GTPase-mediated signal transduction / roof of mouth development / mTORC1-mediated signalling / cellular response to nutrient levels / positive regulation of TOR signaling / response to amino acid / 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 / cellular response to starvation / negative regulation of autophagy / RNA splicing / GTPase activator activity / Regulation of PTEN gene transcription / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein localization / small GTPase binding / GDP binding / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / glucose homeostasis / molecular adaptor activity / lysosome / intracellular signal transduction / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||||||||||||||||||||
![]() | Shen, K. / Huang, R.K. / Brignole, E.J. / Yu, Z. / Sabatini, D.M. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Authors: Kuang Shen / Rick K Huang / Edward J Brignole / Kendall J Condon / Max L Valenstein / Lynne Chantranupong / Aimaiti Bomaliyamu / Abigail Choe / Chuan Hong / Zhiheng Yu / David M Sabatini / ![]() Abstract: Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase- ...Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase. | ||||||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 451.8 KB | Display | ![]() |
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PDB format | ![]() | 349.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 867.8 KB | Display | ![]() |
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Full document | ![]() | 896.8 KB | Display | |
Data in XML | ![]() | 64.2 KB | Display | |
Data in CIF | ![]() | 98.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7464MC ![]() 7465C ![]() 6cetC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-GATOR complex protein ... , 3 types, 3 molecules NMD
#1: Protein | Mass: 43711.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 63680.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 181478.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Ras-related GTP-binding protein ... , 2 types, 2 molecules AC
#4: Protein | Mass: 36615.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 44298.859 Da / Num. of mol.: 1 / Mutation: S75N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/GNP.gif)
#6: Chemical | ChemComp-GNP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: GATOR1-RAG / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.37 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128533 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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