+Open data
-Basic information
Entry | Database: PDB / ID: 6ces | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of GATOR1-RAG | ||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||
Keywords | SIGNALING PROTEIN / mTORC1 amino-acid sensing lysosome growth control | ||||||||||||||||||||||||
Function / homology | Function and homology information GATOR1 complex / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / aorta morphogenesis / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / TORC1 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 / regulation of TOR signaling / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / cardiac muscle tissue development / enzyme-substrate adaptor activity / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / small GTPase-mediated signal transduction / Macroautophagy / roof of mouth development / mTORC1-mediated signalling / positive regulation of TOR signaling / response to amino acid / cellular response to nutrient levels / positive regulation of autophagy / protein-membrane adaptor activity / negative regulation of TORC1 signaling / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / positive regulation of TORC1 signaling / cellular response to starvation / cellular response to amino acid starvation / GTPase activator activity / negative regulation of autophagy / cellular response to amino acid stimulus / RNA splicing / TP53 Regulates Metabolic Genes / phosphoprotein binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / small GTPase binding / GDP binding / protein localization / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / molecular adaptor activity / lysosome / intracellular signal transduction / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / DNA-templated transcription / ubiquitin protein ligase binding / protein-containing complex binding / GTP binding / apoptotic process / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||||||||||||||||||||
Authors | Shen, K. / Huang, R.K. / Brignole, E.J. / Yu, Z. / Sabatini, D.M. | ||||||||||||||||||||||||
Funding support | United States, 7items
| ||||||||||||||||||||||||
Citation | Journal: Nature / Year: 2018 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ces.cif.gz | 451.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ces.ent.gz | 349.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ces.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ces_validation.pdf.gz | 867.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ces_full_validation.pdf.gz | 896.8 KB | Display | |
Data in XML | 6ces_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 6ces_validation.cif.gz | 98.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/6ces ftp://data.pdbj.org/pub/pdb/validation_reports/ce/6ces | HTTPS FTP |
-Related structure data
Related structure data | 7464MC 7465C 6cetC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) Homo sapiens (human) / Gene: NPRL2, TUSC4 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q8WTW4 |
---|---|
#2: Protein | Mass: 63680.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPRL3, C16orf35, CGTHBA, MARE / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q12980 |
#3: Protein | Mass: 181478.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEPDC5, KIAA0645 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: O75140 |
-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.) Homo sapiens (human) / Gene: RRAGA / Plasmid: BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7L523 |
---|---|
#5: Protein | Mass: 44298.859 Da / Num. of mol.: 1 / Mutation: S75N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGC / Plasmid: BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HB90 |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-GNP / |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GATOR1-RAG / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 0.37 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|