+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20814 | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex | ||||||||||||||||||||||||
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Sample |
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Function / homology | Function and homology information negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex ...negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / 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 / negative regulation of brown fat cell differentiation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / negative regulation of cellular respiration / FNIP-folliculin RagC/D GAP / Ragulator complex / regulation of Ras protein signal transduction / protein localization to cell junction / : / regulation of TORC1 signaling / negative regulation of lysosome organization / negative regulation of ATP biosynthetic process / regulation of pro-B cell differentiation / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / ATPase inhibitor activity / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / kinase activator activity / protein localization to membrane / enzyme-substrate adaptor activity / enzyme inhibitor activity / cell-cell junction assembly / negative regulation of glycolytic process / negative regulation of cold-induced thermogenesis / negative regulation of protein localization to nucleus / negative regulation of Rho protein signal transduction / azurophil granule membrane / endosomal transport / Macroautophagy / regulation of cell size / lysosome organization / small GTPase-mediated signal transduction / RHOJ GTPase cycle / TOR signaling / RHOQ GTPase cycle / positive regulation of transforming growth factor beta receptor signaling pathway / mTORC1-mediated signalling / tertiary granule membrane / cellular response to nutrient levels / RHOH GTPase cycle / CDC42 GTPase cycle / hemopoiesis / ficolin-1-rich granule membrane / centriolar satellite / RHOG GTPase cycle / positive regulation of cell adhesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of TOR signaling / regulation of receptor recycling / RAC3 GTPase cycle / RAC2 GTPase cycle / response to amino acid / specific granule membrane / positive regulation of autophagy / energy homeostasis / protein-membrane adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / positive regulation of TORC1 signaling / RAC1 GTPase cycle / tumor necrosis factor-mediated signaling pathway / cellular response to amino acid starvation / cellular response to starvation / GTPase activator activity / guanyl-nucleotide exchange factor activity / intrinsic apoptotic signaling pathway / viral genome replication / negative regulation of autophagy / cholesterol homeostasis / transforming growth factor beta receptor signaling pathway / RNA splicing / negative regulation of cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cytokinesis / Regulation of PTEN gene transcription / epithelial cell proliferation / positive regulation of interleukin-8 production / regulation of cell growth / positive regulation of protein-containing complex assembly / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 Å | ||||||||||||||||||||||||
Authors | Shen K / Rogala KB / Yu ZH / Sabatini DM | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Cell / Year: 2019 Title: Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex. Authors: Kuang Shen / Kacper B Rogala / Hui-Ting Chou / Rick K Huang / Zhiheng Yu / David M Sabatini / Abstract: mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN- ...mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway. | ||||||||||||||||||||||||
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_20814.map.gz | 166.7 MB | EMDB map data format | |
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Header (meta data) | emd-20814-v30.xml emd-20814.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
Images | emd_20814.png | 54.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20814 | HTTPS FTP |
-Related structure data
Related structure data | 6ulgMC M: atomic model generated by this map C: citing same article (ref.) |
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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_20814.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases an...
+Supramolecule #1: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases an...
+Macromolecule #1: Folliculin
+Macromolecule #2: Ragulator complex protein LAMTOR3
+Macromolecule #3: Ragulator complex protein LAMTOR2
+Macromolecule #4: Ragulator complex protein LAMTOR5
+Macromolecule #5: Ragulator complex protein LAMTOR4
+Macromolecule #6: Ragulator complex protein LAMTOR1
+Macromolecule #7: Ras-related GTP-binding protein A
+Macromolecule #8: Ras-related GTP-binding protein C
+Macromolecule #9: Folliculin-interacting protein 2
+Macromolecule #10: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #11: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #12: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 59.2 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: NOT APPLICABLE |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126984 |