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Yorodumi- PDB-6nzd: Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nzd | ||||||
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Title | Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator) | ||||||
Components |
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Keywords | signaling protein/inhibitor / Lysosome / mTORC1 regulation / Amino acid sensing / GTPase / SIGNALING PROTEIN / signaling protein-inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of cell proliferation involved in kidney development / cell proliferation involved in kidney development / negative regulation of post-translational protein modification / 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 ...negative regulation of cell proliferation involved in kidney development / cell proliferation involved in kidney development / negative regulation of post-translational protein modification / 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 / negative regulation of brown fat cell differentiation / regulation of Ras protein signal transduction / protein localization to cell junction / regulation of TORC1 signaling / regulation of pro-B cell differentiation / negative regulation of lysosome organization / protein localization to lysosome / regulation of TOR signaling / TORC1 signaling / endosome organization / fibroblast migration / lysosome localization / Amino acids regulate mTORC1 / ATPase inhibitor activity / MTOR signalling / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / negative regulation of TOR signaling / enzyme inhibitor activity / negative regulation of glycolytic process / cell-cell junction assembly / enzyme-substrate adaptor activity / negative regulation of cold-induced thermogenesis / negative regulation of Rho protein signal transduction / azurophil granule membrane / endosomal transport / small GTPase-mediated signal transduction / regulation of cell size / lysosome organization / Macroautophagy / positive regulation of transforming growth factor beta receptor signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / tertiary granule membrane / hemopoiesis / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / centriolar satellite / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / response to amino acid / RAC2 GTPase cycle / TOR signaling / RAC3 GTPase cycle / cellular response to nutrient levels / specific granule membrane / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of autophagy / protein-membrane adaptor activity / energy homeostasis / tumor necrosis factor-mediated signaling pathway / RAC1 GTPase cycle / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / cellular response to amino acid starvation / ERK1 and ERK2 cascade / cellular response to starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / negative regulation of autophagy / viral genome replication / RNA splicing / transforming growth factor beta receptor signaling pathway / : / epithelial cell proliferation / guanyl-nucleotide exchange factor activity / cholesterol homeostasis / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / regulation of cell growth / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / positive regulation of protein-containing complex assembly / regulation of protein phosphorylation / MAP2K and MAPK activation / response to virus / cilium / mitotic spindle / negative regulation of ERK1 and ERK2 cascade / positive regulation of protein localization to nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of epithelial cell proliferation / GDP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Fromm, S.A. / Young, L.N. / Hurley, J.H. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nzd.cif.gz | 350.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nzd.ent.gz | 265.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nzd_validation.pdf.gz | 901.4 KB | Display | wwPDB validaton report |
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Full document | 6nzd_full_validation.pdf.gz | 925.9 KB | Display | |
Data in XML | 6nzd_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 6nzd_validation.cif.gz | 91.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/6nzd ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nzd | HTTPS FTP |
-Related structure data
Related structure data | 0554MC 0556C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Ragulator complex protein ... , 4 types, 4 molecules ABCD
#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 |
-Protein , 3 types, 3 molecules EHI
#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, UniProt: O43504*PLUS |
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#8: Protein | Mass: 69143.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLCN, BHD / Cell line (production host): HEK 293 GNTI / Production host: Homo sapiens (human) / References: UniProt: Q8NFG4 |
#9: Protein | Mass: 122475.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FNIP2, FNIPL, KIAA1450, MAPO1 / Cell line (production host): HEK 293 GNTI / Production host: Homo sapiens (human) / References: UniProt: Q9P278 |
-Ras-related GTP-binding protein ... , 2 types, 2 molecules FG
#6: Protein | Mass: 36615.168 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 |
-Non-polymers , 2 types, 2 molecules
#10: Chemical | ChemComp-GDP / |
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#11: Chemical | ChemComp-L8S / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: FLCN-FNIP2-RagA-RagC-Ragulator Complex / Type: COMPLEX / Details: RagA bound to GDP; RagC bound to XTPgammaS / Entity ID: #1-#9 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.34 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: 15 W / 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: 90 % / Chamber temperature: 277 K / Details: Whatman 597 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 11 sec. / Electron dose: 65.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2703 |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 44 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 982343 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163376 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 3.6 Å |