+Open data
-Basic information
Entry | Database: PDB / ID: 6ulg | ||||||||||||||||||||||||
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Title | Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex | ||||||||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / FLCN-FNIP2 / Rag GTPases / Ragulator | ||||||||||||||||||||||||
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 / viral genome replication / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / negative regulation of autophagy / cholesterol homeostasis / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / RNA splicing / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å | ||||||||||||||||||||||||
Authors | Shen, K. / Rogala, K.B. / Yu, Z.H. / Sabatini, D.M. | ||||||||||||||||||||||||
Funding support | United States, 7items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ulg.cif.gz | 389.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ulg.ent.gz | 309.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ulg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/6ulg ftp://data.pdbj.org/pub/pdb/validation_reports/ul/6ulg | HTTPS FTP |
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-Related structure data
Related structure data | 20814MC 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
-Protein , 2 types, 2 molecules LN
#1: Protein | Mass: 64551.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLCN, BHD / Production host: Homo sapiens (human) / References: UniProt: Q8NFG4 |
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#9: Protein | Mass: 122260.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FNIP2, FNIPL, KIAA1450, MAPO1 / Production host: Homo sapiens (human) / References: UniProt: Q9P278 |
-Ragulator complex protein ... , 5 types, 5 molecules ABCDE
#2: 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: Escherichia coli (E. coli) / References: UniProt: Q9UHA4 |
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#3: Protein | Mass: 13517.450 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: Escherichia coli (E. coli) / References: UniProt: Q9Y2Q5 |
#4: Protein | Mass: 9622.900 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Production host: Escherichia coli (E. coli) / References: UniProt: O43504 |
#5: 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: Escherichia coli (E. coli) / References: UniProt: Q0VGL1 |
#6: Protein | Mass: 17762.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IAA8 |
-Ras-related GTP-binding protein ... , 2 types, 2 molecules FG
#7: Protein | Mass: 36628.168 Da / Num. of mol.: 1 / Mutation: T21N Source method: isolated from a genetically manipulated source Details: RagA containing a T21N mutation / Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L523 |
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#8: Protein | Mass: 44271.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HB90 |
-Non-polymers , 3 types, 3 molecules
#10: Chemical | ChemComp-GDP / |
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#11: Chemical | ChemComp-GNP / |
#12: Chemical | ChemComp-MG / |
-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
Component | Name: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases and the scaffolding protein complex Ragulator Type: COMPLEX / Entity ID: #1-#9 / Source: RECOMBINANT |
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Molecular weight | Value: 0.38 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 59.2 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126984 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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