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Yorodumi- PDB-6wj3: CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wj3 | ||||||
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Title | CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the post-GAP state | ||||||
Components |
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Keywords | SIGNALING PROTEIN / small GTPase / mTORC1 activation / amino acid signaling / lysosome | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Fromm, S.A. / Hurley, J.H. | ||||||
Funding support | United States, 1items
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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 |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wj3.cif.gz | 224.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wj3.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wj3_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6wj3_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6wj3_validation.xml.gz | 49 KB | Display | |
Data in CIF | 6wj3_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/6wj3 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wj3 | HTTPS FTP |
-Related structure data
Related structure data | 21687MC 6wj2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Ragulator complex protein ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 18325.350 Da / Num. of mol.: 1 / Mutation: G2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6IAA8 |
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#2: Protein | Mass: 13645.579 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR2, MAPBPIP, ROBLD3, HSPC003 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2Q5 |
#3: Protein | Mass: 13637.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UHA4 |
#4: Protein | Mass: 10753.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q0VGL1 |
#5: Protein | Mass: 18178.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, hCG_40252 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0C4DGV4 |
-Ras-related GTP-binding protein ... , 2 types, 2 molecules FG
#6: Protein | Mass: 39362.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L523 |
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#7: Protein | Mass: 44758.336 Da / Num. of mol.: 1 / Mutation: D181N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HB90 |
-Protein , 1 types, 1 molecules H
#8: Protein | Mass: 13610.139 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC38A9, URLC11 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8NBW4 |
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-Non-polymers , 2 types, 2 molecules
#9: Chemical | ChemComp-GDP / |
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#10: Chemical | ChemComp-U3J / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.17 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
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Source (recombinant) |
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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 5.7 sec. / Electron dose: 60.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
-Processing
Software | Name: PHENIX / Version: dev_3736: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2309565 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106659 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||
Refine LS restraints |
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