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- PDB-9h4q: Cryo-EM structure of the SEAC wing - EGOC -

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Basic information

Entry
Database: PDB / ID: 9h4q
TitleCryo-EM structure of the SEAC wing - EGOC
Components
  • (GTP-binding protein ...) x 2
  • (Nitrogen permease regulator ...) x 2
  • Maintenance of telomere capping protein 5
  • Protein EGO2
  • Protein MEH1
  • Protein SLM4
  • Vacuolar membrane-associated protein IML1
KeywordsSIGNALING PROTEIN / GTPase activating protein / GTPase / nutrient-sensing / amino acid signaling / cell growth
Function / homology
Function and homology information


MTOR signalling / GATOR1 complex / pseudohyphal growth / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole ...MTOR signalling / GATOR1 complex / pseudohyphal growth / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole / Seh1-associated complex / Amino acids regulate mTORC1 / proline transport / regulation of TORC1 signaling / phosphate ion transport / regulation of autophagosome assembly / endocytic recycling / vacuolar acidification / fungal-type vacuole membrane / negative regulation of TOR signaling / cellular response to nitrogen starvation / vacuolar membrane / TORC1 signaling / transcription by RNA polymerase III / regulation of receptor recycling / positive regulation of TOR signaling / subtelomeric heterochromatin formation / transcription by RNA polymerase I / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / positive regulation of autophagy / signaling adaptor activity / negative regulation of autophagy / GTPase activator activity / cellular response to amino acid starvation / cellular response to starvation / meiotic cell cycle / cellular response to amino acid stimulus / late endosome / late endosome membrane / protein transport / cellular response to oxidative stress / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / chromosome, telomeric region / positive regulation of MAPK cascade / intracellular signal transduction / membrane raft / response to xenobiotic stimulus / GTPase activity / chromatin / GTP binding / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / : / : / RING/Ubox like zinc-binding domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 ...YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / : / : / RING/Ubox like zinc-binding domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / : / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / GATOR1 complex protein NPRL3, C-terminal HTH / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / Vacuolar membrane-associated protein Iml1, N-terminal domain / DEPDC5 protein C-terminal region / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / RagA/B / RWD domain / RagC/D / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / RWD domain profile. / RWD / RWD domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / WD domain, G-beta repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Protein SLM4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / GTP-binding protein GTR2 / GTP-binding protein GTR1 / Protein MEH1 / Maintenance of telomere capping protein 5 / Protein EGO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTafur, L. / Loewith, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)AdG TENDOEuropean Union
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: 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.
History
DepositionOct 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Maintenance of telomere capping protein 5
a: GTP-binding protein GTR1
c: GTP-binding protein GTR2
T: Nitrogen permease regulator 2
h: Nitrogen permease regulator 3
X: Vacuolar membrane-associated protein IML1
R: Protein MEH1
U: Protein EGO2
Y: Protein SLM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)635,65013
Polymers634,6559
Non-polymers9954
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 5 molecules CXRUY

#1: Protein Maintenance of telomere capping protein 5 / SEH-associated protein 3


Mass: 131104.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03897
#6: Protein Vacuolar membrane-associated protein IML1 / Increased minichromosome loss protein 1 / SEH-associated protein 1


Mass: 182203.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47170
#7: Protein Protein MEH1 / EGO complex subunit 1 / GSE complex subunit 2


Mass: 20266.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MEH1, EGO1, GSE2, YKR007W, YK106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02205
#8: Protein Protein EGO2


Mass: 8104.935 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EGO2, YCR075W-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q3E830
#9: Protein Protein SLM4 / EGO complex subunit 3 / GSE complex subunit 1


Mass: 18371.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLM4, EGO3, GSE1, YBR077C, YBR0723 / Production host: Escherichia coli (E. coli) / References: UniProt: P38247

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GTP-binding protein ... , 2 types, 2 molecules ac

#2: Protein GTP-binding protein GTR1


Mass: 35892.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GTR1, YML121W, YM7056.05 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00582, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Protein GTP-binding protein GTR2


Mass: 38633.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GTR2, YGR163W / Production host: Escherichia coli (E. coli)
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, 2 molecules Th

#4: Protein Nitrogen permease regulator 2


Mass: 69937.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39923
#5: Protein Nitrogen permease regulator 3 / Required for meiotic nuclear division protein 11


Mass: 130141.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38742

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Non-polymers , 3 types, 4 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SEAC-EGOC supercomplexCOMPLEX#1-#90NATURAL
2SEA complex wingCOMPLEX#1, #4-#61NATURAL
3EGO complexCOMPLEX#2-#3, #7-#91RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
43Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF Chimera1.7model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133077 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18ae6

8ae6

18ae61PDBexperimental model
21AlphaFoldin silico model
36jwp

6jwp

16jwp3PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328093
ELECTRON MICROSCOPYf_angle_d0.57837995
ELECTRON MICROSCOPYf_dihedral_angle_d4.5143642
ELECTRON MICROSCOPYf_chiral_restr0.0464230
ELECTRON MICROSCOPYf_plane_restr0.0054808

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