+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27435 | |||||||||||||||
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Title | Active FLCN GAP complex | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | FLCN / Rag-Ragulator / GTPase Activating Protein / mTORC1 signaling / SIGNALING PROTEIN | |||||||||||||||
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 / glutathione transferase / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / centriolar satellite / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutathione transferase activity / 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 / glutathione metabolic process / 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 Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.53 Å | |||||||||||||||
Authors | Jansen RM / Hurley JH | |||||||||||||||
Funding support | United States, Italy, 4 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Structural basis for FLCN RagC GAP activation in MiT-TFE substrate-selective mTORC1 regulation. Authors: Rachel M Jansen / Roberta Peruzzo / Simon A Fromm / Adam L Yokom / Roberto Zoncu / James H Hurley / Abstract: The mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and catabolism in response to nutrients through phosphorylation of key substrates. The tumor suppressor folliculin (FLCN) ...The mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth and catabolism in response to nutrients through phosphorylation of key substrates. The tumor suppressor folliculin (FLCN) is a RagC/D guanosine triphosphatase (GTPase)-activating protein (GAP) that regulates mTORC1 phosphorylation of MiT-TFE transcription factors, controlling lysosome biogenesis and autophagy. We determined the cryo-electron microscopy structure of the active FLCN complex (AFC) containing FLCN, FNIP2, the N-terminal tail of SLC38A9, the RagA:RagC GTPase dimer, and the Ragulator scaffold. Relative to the inactive lysosomal FLCN complex structure, FLCN reorients by 90°, breaks contact with RagA, and makes previously unseen contacts with RagC that position its Arg finger for catalysis. Disruption of the AFC-specific interfaces of FLCN and FNIP2 with RagC eliminated GAP activity and led to nuclear retention of TFE3, with no effect on mTORC1 substrates S6K or 4E-BP1. The structure provides a basis for regulation of an mTORC1 substrate-specific pathway and a roadmap to discover MiT-TFE family selective mTORC1 antagonists. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27435.map.gz | 306.8 MB | EMDB map data format | |
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Header (meta data) | emd-27435-v30.xml emd-27435.xml | 32.3 KB 32.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27435_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_27435.png | 62.8 KB | ||
Filedesc metadata | emd-27435.cif.gz | 8.6 KB | ||
Others | emd_27435_additional_1.map.gz emd_27435_half_map_1.map.gz emd_27435_half_map_2.map.gz | 306.6 MB 301.9 MB 301.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27435 | HTTPS FTP |
-Validation report
Summary document | emd_27435_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27435_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27435_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | emd_27435_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27435 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27435 | HTTPS FTP |
-Related structure data
Related structure data | 8dhbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27435.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Focused refinement at FLCN:RagC interface
File | emd_27435_additional_1.map | ||||||||||||
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Annotation | Focused refinement at FLCN:RagC interface | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27435_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27435_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of the Active FLCN GAP compex
+Supramolecule #1: Cryo-EM structure of the Active FLCN GAP compex
+Supramolecule #2: Rag-Ragulator
+Supramolecule #3: FLCN:SLC-FNIP2
+Macromolecule #1: Ras-related GTP-binding protein C
+Macromolecule #2: Ras-related GTP-binding protein A
+Macromolecule #3: Ragulator complex protein LAMTOR1
+Macromolecule #4: Ragulator complex protein LAMTOR2
+Macromolecule #5: Ragulator complex protein LAMTOR3
+Macromolecule #6: Ragulator complex protein LAMTOR4
+Macromolecule #7: Ragulator complex protein LAMTOR5
+Macromolecule #8: Glutathione S-transferase class-mu 26 kDa isozyme,Sodium-coupled ...
+Macromolecule #9: Folliculin-interacting protein 2
+Macromolecule #10: Folliculin
+Macromolecule #11: [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-...
+Macromolecule #12: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #13: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |