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Yorodumi- EMDB-21687: CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in th... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21687 | |||||||||
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Title | CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the post-GAP state | |||||||||
Map data | Ragulator-RagA-GDP-RagC-XDP-SLC38A9; density modified with LocScale | |||||||||
Sample |
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Keywords | small GTPase / mTORC1 activation / amino acid signaling / lysosome / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity / L-arginine transmembrane transporter activity / L-arginine transmembrane transport / 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 ...asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity / L-arginine transmembrane transporter activity / L-arginine transmembrane transport / 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 / L-glutamine transmembrane transporter activity / FNIP-folliculin RagC/D GAP / Ragulator complex / glutamine transport / L-amino acid transmembrane transporter activity / L-leucine transmembrane transporter activity / protein localization to cell junction / amino acid transmembrane transport / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / amino acid transmembrane transporter activity / TORC1 signaling / endosome organization / fibroblast migration / Amino acids regulate mTORC1 / MTOR signalling / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / arginine binding / enzyme-substrate adaptor activity / azurophil granule membrane / endosomal transport / cholesterol binding / small GTPase-mediated signal transduction / regulation of cell size / lysosome organization / Macroautophagy / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / tertiary granule membrane / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / RAC2 GTPase cycle / response to amino acid / RAC3 GTPase cycle / cellular response to nutrient levels / specific granule membrane / protein-membrane adaptor activity / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / positive regulation of TORC1 signaling / cellular response to amino acid starvation / cellular response to starvation / RNA splicing / viral genome replication / negative regulation of autophagy / : / cholesterol homeostasis / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / regulation of cell growth / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / MAP2K and MAPK activation / response to virus / positive regulation of protein localization to nucleus / GDP binding / protein localization / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / late endosome membrane / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / intracellular signal transduction / protein heterodimerization activity / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / DNA-templated transcription / ubiquitin protein ligase binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Fromm SA / Hurley JH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structural mechanism for amino acid-dependent Rag GTPase nucleotide state switching by SLC38A9. Authors: Simon A Fromm / Rosalie E Lawrence / James H Hurley / Abstract: The Rag GTPases (Rags) recruit mTORC1 to the lysosomal membrane in response to nutrients, where it is then activated in response to energy and growth factor availability. The lysosomal folliculin ...The Rag GTPases (Rags) recruit mTORC1 to the lysosomal membrane in response to nutrients, where it is then activated in response to energy and growth factor availability. The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator, and the FLCN:FNIP2 (FLCN-interacting protein 2) GTPase activating protein (GAP) complex, and prevents Rag dimer activation during amino acid starvation. How the LFC is disassembled upon amino acid refeeding is an outstanding question. Here we show that the cytoplasmic tail of the human lysosomal solute carrier family 38 member 9 (SLC38A9) destabilizes the LFC and thereby triggers GAP activity of FLCN:FNIP2 toward RagC. We present the cryo-EM structures of Rags in complex with their lysosomal anchor complex Ragulator and the cytoplasmic tail of SLC38A9 in the pre- and post-GTP hydrolysis state of RagC, which explain how SLC38A9 destabilizes the LFC and so promotes Rag dimer activation. | |||||||||
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_21687.map.gz | 1.8 MB | EMDB map data format | |
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Header (meta data) | emd-21687-v30.xml emd-21687.xml | 27 KB 27 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21687_fsc.xml | 10.1 KB | Display | FSC data file |
Images | emd_21687.png | 112.4 KB | ||
Masks | emd_21687_msk_1.map emd_21687_msk_2.map | 91.1 MB 91.1 MB | Mask map | |
Filedesc metadata | emd-21687.cif.gz | 7.3 KB | ||
Others | emd_21687_half_map_1.map.gz emd_21687_half_map_2.map.gz | 84.5 MB 84.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21687 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21687 | HTTPS FTP |
-Validation report
Summary document | emd_21687_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_21687_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_21687_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_21687_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21687 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21687 | HTTPS FTP |
-Related structure data
Related structure data | 6wj3MC 6wj2C 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_21687.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ragulator-RagA-GDP-RagC-XDP-SLC38A9; density modified with LocScale | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.137 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21687_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_21687_msk_2.map | ||||||||||||
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Density Histograms |
-Half map: half map A
File | emd_21687_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_21687_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9
+Supramolecule #1: Complex of pentameric Ragulator, dimeric Rag GTPases and SLC38A9
+Supramolecule #2: pentameric Ragulator
+Supramolecule #3: dimeric Rag GTPases
+Supramolecule #4: SLC38A9
+Macromolecule #1: Ragulator complex protein LAMTOR1
+Macromolecule #2: Ragulator complex protein LAMTOR2
+Macromolecule #3: Ragulator complex protein LAMTOR3
+Macromolecule #4: Ragulator complex protein LAMTOR4
+Macromolecule #5: Ragulator complex protein LAMTOR5
+Macromolecule #6: Ras-related GTP-binding protein A
+Macromolecule #7: Ras-related GTP-binding protein C
+Macromolecule #8: Sodium-coupled neutral amino acid transporter 9
+Macromolecule #9: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #10: xanthosine diphosphate
-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 |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 5.7 sec. / Average electron dose: 60.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6wj3: |