+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20660 | |||||||||||||||||||||||||||
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Title | Raptor-Rag-Ragulator complex | |||||||||||||||||||||||||||
Map data | Unmasked, unsharpened. | |||||||||||||||||||||||||||
Sample |
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Keywords | signaling complex / GTPase / lysosome / SIGNALING PROTEIN | |||||||||||||||||||||||||||
Function / homology | Function and homology information 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 / protein localization to cell junction / positive regulation of pentose-phosphate shunt ...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 / protein localization to cell junction / positive regulation of pentose-phosphate shunt / regulation of TORC1 signaling / TORC1 complex / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / positive regulation of odontoblast differentiation / endosome organization / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein serine/threonine kinase inhibitor activity / kinase activator activity / cellular response to osmotic stress / positive regulation of osteoclast differentiation / protein localization to membrane / enzyme-substrate adaptor activity / positive regulation of transcription by RNA polymerase III / azurophil granule membrane / endosomal transport / Macroautophagy / regulation of cell size / lysosome organization / small GTPase-mediated signal transduction / protein kinase activator activity / RHOJ GTPase cycle / TOR signaling / RHOQ GTPase cycle / mTORC1-mediated signalling / social behavior / tertiary granule membrane / cellular response to nutrient levels / RHOH GTPase cycle / CDC42 GTPase cycle / ficolin-1-rich granule membrane / HSF1-dependent transactivation / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / positive regulation of G1/S transition of mitotic cell cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / response to amino acid / positive regulation of lipid biosynthetic process / specific granule membrane / protein-membrane adaptor activity / positive regulation of TORC1 signaling / RAC1 GTPase cycle / tumor necrosis factor-mediated signaling pathway / cellular response to amino acid starvation / cellular response to starvation / positive regulation of endothelial cell proliferation / positive regulation of glycolytic process / viral genome replication / guanyl-nucleotide exchange factor activity / negative regulation of autophagy / cholesterol homeostasis / RNA splicing / 14-3-3 protein binding / positive regulation of peptidyl-threonine phosphorylation / Regulation of PTEN gene transcription / regulation of autophagy / positive regulation of interleukin-8 production / regulation of cell growth / cellular response to glucose stimulus / 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 / cytoplasmic stress granule / positive regulation of protein localization to nucleus / GDP binding / protein-macromolecule adaptor activity / late endosome / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / positive regulation of peptidyl-serine phosphorylation / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / positive regulation of cell growth / positive regulation of canonical NF-kappaB signal transduction Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||||||||||||||||||||
Authors | Rogala KB / Sabatini DM | |||||||||||||||||||||||||||
Funding support | United States, United Kingdom, 8 items
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Citation | Journal: Science / Year: 2019 Title: Structural basis for the docking of mTORC1 on the lysosomal surface. Authors: Kacper B Rogala / Xin Gu / Jibril F Kedir / Monther Abu-Remaileh / Laura F Bianchi / Alexia M S Bottino / Rikke Dueholm / Anna Niehaus / Daan Overwijn / Ange-Célia Priso Fils / Sherry X ...Authors: Kacper B Rogala / Xin Gu / Jibril F Kedir / Monther Abu-Remaileh / Laura F Bianchi / Alexia M S Bottino / Rikke Dueholm / Anna Niehaus / Daan Overwijn / Ange-Célia Priso Fils / Sherry X Zhou / Daniel Leary / Nouf N Laqtom / Edward J Brignole / David M Sabatini / Abstract: The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where ...The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20660.map.gz | 132 MB | EMDB map data format | |
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Header (meta data) | emd-20660-v30.xml emd-20660.xml | 24 KB 24 KB | Display Display | EMDB header |
Images | emd_20660.png | 120 KB | ||
Filedesc metadata | emd-20660.cif.gz | 7.6 KB | ||
Others | emd_20660_additional.map.gz | 154.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20660 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20660 | HTTPS FTP |
-Related structure data
Related structure data | 6u62MC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20660.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unmasked, unsharpened. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unmasked, sharpened.
File | emd_20660_additional.map | ||||||||||||
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Annotation | Unmasked, sharpened. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Raptor-Rag-Ragulator
+Supramolecule #1: Raptor-Rag-Ragulator
+Macromolecule #1: Regulatory-associated protein of mTOR
+Macromolecule #2: Ras-related GTP-binding protein A
+Macromolecule #3: Ras-related GTP-binding protein C
+Macromolecule #4: Ragulator complex protein LAMTOR1
+Macromolecule #5: Ragulator complex protein LAMTOR2
+Macromolecule #6: Ragulator complex protein LAMTOR3
+Macromolecule #7: Ragulator complex protein LAMTOR4
+Macromolecule #8: Ragulator complex protein LAMTOR5
+Macromolecule #9: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112037 |