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Open data
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Basic information
Entry | Database: PDB / ID: 7uhy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Title | Human GATOR2 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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![]() | SIGNALING PROTEIN / mTOR / GATOR / lysosome / nutrient sensing / complex / zinc finger / ZnF / RING / C2 symmetry / octagon | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() GATOR2 complex / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / Amino acids regulate mTORC1 ...GATOR2 complex / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / COPII-mediated vesicle transport / Viral Messenger RNA Synthesis / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / cellular response to nutrient levels / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / cellular response to amino acid starvation / SUMOylation of chromatin organization proteins / HCMV Late Events / regulation of autophagy / RHO GTPases Activate Formins / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / intracellular protein transport / ER to Golgi transport vesicle membrane / ISG15 antiviral mechanism / kinetochore / autophagy / HCMV Early Events / Separation of Sister Chromatids / protein import into nucleus / protein transport / cell junction / nuclear envelope / snRNP Assembly / defense response to Gram-positive bacterium / cell division / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
![]() | Rogala, K.B. / Valenstein, M.L. / Lalgudi, P.V. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the nutrient-sensing hub GATOR2. Authors: Max L Valenstein / Kacper B Rogala / Pranav V Lalgudi / Edward J Brignole / Xin Gu / Robert A Saxton / Lynne Chantranupong / Jonas Kolibius / Jan-Philipp Quast / David M Sabatini / ![]() Abstract: Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients. Amino acids signal to mTORC1 ...Mechanistic target of rapamycin complex 1 (mTORC1) controls growth by regulating anabolic and catabolic processes in response to environmental cues, including nutrients. Amino acids signal to mTORC1 through the Rag GTPases, which are regulated by several protein complexes, including GATOR1 and GATOR2. GATOR2, which has five components (WDR24, MIOS, WDR59, SEH1L and SEC13), is required for amino acids to activate mTORC1 and interacts with the leucine and arginine sensors SESN2 and CASTOR1, respectively. Despite this central role in nutrient sensing, GATOR2 remains mysterious as its subunit stoichiometry, biochemical function and structure are unknown. Here we used cryo-electron microscopy to determine the three-dimensional structure of the human GATOR2 complex. We found that GATOR2 adopts a large (1.1 MDa), two-fold symmetric, cage-like architecture, supported by an octagonal scaffold and decorated with eight pairs of WD40 β-propellers. The scaffold contains two WDR24, four MIOS and two WDR59 subunits circularized via two distinct types of junction involving non-catalytic RING domains and α-solenoids. Integration of SEH1L and SEC13 into the scaffold through β-propeller blade donation stabilizes the GATOR2 complex and reveals an evolutionary relationship to the nuclear pore and membrane-coating complexes. The scaffold orients the WD40 β-propeller dimers, which mediate interactions with SESN2, CASTOR1 and GATOR1. Our work reveals the structure of an essential component of the nutrient-sensing machinery and provides a foundation for understanding the function of GATOR2 within the mTORC1 pathway. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 632 KB | Display | ![]() |
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PDB format | ![]() | 485.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 97.3 KB | Display | |
Data in CIF | ![]() | 150.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26519MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-GATOR complex protein ... , 3 types, 4 molecules ABCD
#1: Protein | Mass: 100633.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | | Mass: 88326.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | | Mass: 109938.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein , 2 types, 4 molecules EFGH
#4: Protein | Mass: 46636.289 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | | Mass: 35578.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein/peptide , 2 types, 2 molecules IJ
#6: Protein/peptide | Mass: 1294.587 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#7: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 1 types, 16 molecules ![](data/chem/img/ZN.gif)
#8: Chemical | ChemComp-ZN / |
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-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 |
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Sample preparation
Component | Name: Human GATOR2 / Type: COMPLEX Details: Purified five-component GATOR2 complex via a Flag-tag on MIOS. Entity ID: #1-#7 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.1 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 95% pure, monodisperse protein complex. Partial loss of a few subunits observed. Contaminating CCT chaperonin present. | ||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
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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: ![]() | ||||||||||||||||||
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 45779 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE | ||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||
Image recording | Imaging-ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
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EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Movie frames were weighted according to electron dose and particle movement. Please note that the two datasets collected at (1) UMass and (2) MIT.nano were eventually pixel-size-matched and ...Details: Movie frames were weighted according to electron dose and particle movement. Please note that the two datasets collected at (1) UMass and (2) MIT.nano were eventually pixel-size-matched and merged into a single dataset. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 7237873 Details: The reported particle number is the sum of particles from two datasets, including parallel picking strategies. See details in the methods section of Valenstein and Rogala et al (2022). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 784651 / Algorithm: FOURIER SPACE / Details: Duplicate particles were removed. / Num. of class averages: 5 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 182 / Protocol: OTHER / Space: REAL Details: Most of the structure was built de novo in Coot. WD40 propellers were rebuilt after fitting either deposited PDB coordinates of homologous structures or predicted models from RoseTTAFold. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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