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Open data
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Basic information
| Entry | Database: PDB / ID: 9h5k | |||||||||||||||||||||||||||||||||
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| Title | Cryo-EM structure of the SEAC-EGOC supercomplex | |||||||||||||||||||||||||||||||||
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Keywords | SIGNALING PROTEIN / Cell growth / GTPase activating protein / GTPase / coatomer complex | |||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationMTOR signalling / GATOR1 complex / Gtr1-Gtr2 GTPase complex / urea transport / GATOR2 complex / pseudohyphal growth / negative regulation of small GTPase mediated signal transduction / Ragulator complex / microautophagy / protein localization to vacuole ...MTOR signalling / GATOR1 complex / Gtr1-Gtr2 GTPase complex / urea transport / GATOR2 complex / pseudohyphal growth / negative regulation of small GTPase mediated signal transduction / Ragulator complex / microautophagy / protein localization to vacuole / protein localization to vacuolar membrane / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / COPII-coated vesicle budding / nuclear pore localization / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / regulation of TORC1 signaling / Regulation of Glucokinase by Glucokinase Regulatory Protein / Amino acids regulate mTORC1 / proline transport / : / nuclear pore outer ring / Regulation of HSF1-mediated heat shock response / COPII vesicle coat / phosphate ion transport / positive regulation of protein exit from endoplasmic reticulum / fungal-type vacuole / regulation of autophagosome assembly / SUMOylation of SUMOylation proteins / endocytic recycling / structural constituent of nuclear pore / vacuolar acidification / negative regulation of TOR signaling / SUMOylation of RNA binding proteins / fungal-type vacuole membrane / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / nucleocytoplasmic transport / vacuolar membrane / TORC1 signaling / positive regulation of macroautophagy / regulation of receptor recycling / endoplasmic reticulum exit site / subtelomeric heterochromatin formation / transcription by RNA polymerase III / nuclear pore / positive regulation of TOR signaling / mRNA transport / transcription by RNA polymerase I / negative regulation of TORC1 signaling / ERAD pathway / positive regulation of TORC1 signaling / signaling adaptor activity / positive regulation of autophagy / cellular response to amino acid starvation / cellular response to starvation / negative regulation of autophagy / GTPase activator activity / cell periphery / cellular response to amino acid stimulus / meiotic cell cycle / protein import into nucleus / late endosome / nuclear envelope / late endosome membrane / protein transport / cellular response to oxidative stress / nuclear membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of MAPK cascade / chromosome, telomeric region / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / GTPase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / GTP binding / chromatin / structural molecule activity / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||
| Biological species | ![]() | |||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||||||||||||||
Authors | Tafur, L. / Loewith, R. | |||||||||||||||||||||||||||||||||
| Funding support | European Union, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2026Title: Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex. Authors: Lucas Tafur / Lenny Bonadei / Yiqiang Zheng / Caroline Gabus / Robbie Loewith / ![]() Abstract: The Seh1-associated complex (SEAC; GATOR in mammals) transduces amino acid signals to the Target of Rapamycin Complex 1 (TORC1), a master regulator of cell growth. The SEAC is composed of two ...The Seh1-associated complex (SEAC; GATOR in mammals) transduces amino acid signals to the Target of Rapamycin Complex 1 (TORC1), a master regulator of cell growth. The SEAC is composed of two subcomplexes, SEACIT (GATOR1), an inhibitor of TORC1 that has GAP activity against Gtr1, and SEACAT (GATOR2), which appears to regulate SEACIT. However, the molecular details of this regulation are unclear. Here we determined the cryo-electron microscopy structure of the SEAC bound to its substrate, the EGOC (Ragulator-Rag), and studied its function in TORC1 amino acid signaling. A single SEAC can interact with two EGOC molecules via SEACIT, binding exclusively to the 'active' version of the EGOC, without involvement of SEACAT. The GAP activity of the SEACIT is essential for the regulation of TORC1 by amino acids and its loss phenocopies the lack of Gtr1-Gtr2, establishing the SEAC-EGOC complex as an amino acid-sensing hub. Compared to other SEACAT subunits, the loss of Sea2, or its N-terminal β-propeller domain, yielded strong defects in amino acid signaling to TORC1. Our results suggest that the Sea2 β-propeller recruits a GAP inhibitor to mediate fast amino acid signaling to TORC1, with additional pathways acting with slower kinetics. | |||||||||||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9h5k.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9h5k.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9h5k.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/9h5k ftp://data.pdbj.org/pub/pdb/validation_reports/h5/9h5k | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 51887MC ![]() 9h4qC C: citing same article ( M: map data used to model this data |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-Protein , 9 types, 24 molecules CKHPAIFEDNMLGBOJXjRSUWYZ
| #1: Protein | Mass: 131104.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 33082.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 149533.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 39170.758 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 117775.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 182203.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 20266.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MEH1, EGO1, GSE2, YKR007W, YK106 / Production host: ![]() #12: Protein | Mass: 8104.935 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: EGO2, YCR075W-A / Production host: ![]() #13: Protein | Mass: 18371.877 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SLM4, EGO3, GSE1, YBR077C, YBR0723 / Production host: ![]() |
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-GTP-binding protein ... , 2 types, 4 molecules abcd
| #6: Protein | Mass: 35892.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: GTR1, YML121W, YM7056.05 / Production host: ![]() References: UniProt: Q00582, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #7: Protein | Mass: 38633.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: GTR2, YGR163W / Production host: ![]() References: UniProt: P53290, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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-Nitrogen permease regulator ... , 2 types, 4 molecules Tghi
| #8: Protein | Mass: 69937.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 130141.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 4 types, 36 molecules 






| #14: Chemical | ChemComp-ZN / #15: Chemical | #16: Chemical | #17: Chemical | ChemComp-GDP / |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | N |
-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
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| Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
| Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm |
| Image recording | Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208039 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
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About Yorodumi






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FIELD EMISSION GUN

