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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 transport / L-arginine transmembrane transporter activity / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / glutamine transport / L-glutamine transmembrane transporter activity ...asparagine transport / L-asparagine transmembrane transporter activity / sterol sensor activity / L-arginine transmembrane transport / L-arginine transmembrane transporter activity / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / glutamine transport / L-glutamine transmembrane transporter activity / 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 / L-amino acid transmembrane transporter activity / L-leucine transmembrane transporter activity / amino acid transmembrane transport / protein localization to cell junction / regulation of TORC1 signaling / amino acid transmembrane transporter activity / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / enzyme-substrate adaptor activity / arginine binding / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / small GTPase-mediated signal transduction / lysosome organization / cholesterol binding / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / specific granule membrane / protein-membrane adaptor activity / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / cellular response to amino acid starvation / cellular response to starvation / negative regulation of autophagy / viral genome replication / RNA splicing / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / 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 / response to virus / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / positive regulation of protein localization to nucleus / GDP binding / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / glucose homeostasis / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / intracellular signal transduction / membrane raft / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / GTPase activity / DNA-templated transcription / apoptotic process 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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Projections & Slices |
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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: |