+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0556 | |||||||||
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Title | Cryo-EM Map of the active Ragulator-RagA-RagC Complex | |||||||||
Map data | em-volume_P1 | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex ...negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / 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 / negative regulation of brown fat cell differentiation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / negative regulation of cellular respiration / FNIP-folliculin RagC/D GAP / Ragulator complex / regulation of Ras protein signal transduction / protein localization to cell junction / : / regulation of TORC1 signaling / negative regulation of lysosome organization / negative regulation of ATP biosynthetic process / regulation of pro-B cell differentiation / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / ATPase inhibitor activity / 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 / protein localization to membrane / enzyme-substrate adaptor activity / enzyme inhibitor activity / cell-cell junction assembly / negative regulation of glycolytic process / negative regulation of cold-induced thermogenesis / negative regulation of protein localization to nucleus / negative regulation of Rho protein signal transduction / azurophil granule membrane / endosomal transport / Macroautophagy / regulation of cell size / lysosome organization / small GTPase-mediated signal transduction / RHOJ GTPase cycle / TOR signaling / RHOQ GTPase cycle / positive regulation of transforming growth factor beta receptor signaling pathway / mTORC1-mediated signalling / tertiary granule membrane / cellular response to nutrient levels / RHOH GTPase cycle / CDC42 GTPase cycle / hemopoiesis / ficolin-1-rich granule membrane / centriolar satellite / RHOG GTPase cycle / positive regulation of cell adhesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of TOR signaling / regulation of receptor recycling / RAC3 GTPase cycle / RAC2 GTPase cycle / response to amino acid / specific granule membrane / positive regulation of autophagy / energy homeostasis / protein-membrane adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / positive regulation of TORC1 signaling / RAC1 GTPase cycle / tumor necrosis factor-mediated signaling pathway / cellular response to amino acid starvation / cellular response to starvation / GTPase activator activity / viral genome replication / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / negative regulation of autophagy / cholesterol homeostasis / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cytokinesis / Regulation of PTEN gene transcription / epithelial cell proliferation / positive regulation of interleukin-8 production / regulation of cell growth / positive regulation of protein-containing complex assembly / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.1 Å | |||||||||
Authors | Yokom AL / Fromm SA / Hurley JH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2019 Title: Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex. Authors: Rosalie E Lawrence / Simon A Fromm / Yangxue Fu / Adam L Yokom / Do Jin Kim / Ashley M Thelen / Lindsey N Young / Chun-Yan Lim / Avi J Samelson / James H Hurley / Roberto Zoncu / Abstract: The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) ...The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) activating protein (GAP) activity toward the GTPase RagC. Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. To determine the lysosomal function of FLCN, we reconstituted the human lysosomal FLCN complex (LFC) containing FLCN, its partner FLCN-interacting protein 2 (FNIP2), and the RagA:RagC GTPases as they exist in the starved state with their lysosomal anchor Ragulator complex and determined its cryo-electron microscopy structure to 3.6 angstroms. The RagC-GAP activity of FLCN was inhibited within the LFC, owing to displacement of a catalytically required arginine in FLCN from the RagC nucleotide. Disassembly of the LFC and release of the RagC-GAP activity of FLCN enabled mTORC1-dependent regulation of the master regulator of lysosomal biogenesis, transcription factor E3, implicating the LFC as a checkpoint in mTORC1 signaling. | |||||||||
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_0556.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-0556-v30.xml emd-0556.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_0556.png | 43.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0556 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0556 | HTTPS FTP |
-Related 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_0556.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | em-volume_P1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.149 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : active RagA-RagC-Ragulator Complex
Entire | Name: active RagA-RagC-Ragulator Complex |
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Components |
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-Supramolecule #1: active RagA-RagC-Ragulator Complex
Supramolecule | Name: active RagA-RagC-Ragulator Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 Details: RagA bound to GTP; RagC bound to XDP RagC has T90N and D181N mutations |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 |
Molecular weight | Theoretical: 150 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Startup model | Type of model: NONE / Details: cryoSPARC v2 ab-initio |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 75996 |