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- PDB-9h5k: Cryo-EM structure of the SEAC-EGOC supercomplex -

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Basic information

Entry
Database: PDB / ID: 9h5k
TitleCryo-EM structure of the SEAC-EGOC supercomplex
Components
  • (GTP-binding protein ...) x 2
  • (Nitrogen permease regulator ...) x 2
  • Maintenance of telomere capping protein 5
  • Nucleoporin SEH1
  • Protein EGO2
  • Protein MEH1
  • Protein SLM4
  • Protein transport protein SEC13
  • Restriction of telomere capping protein 1
  • SEH-associated protein 4
  • Vacuolar membrane-associated protein IML1
KeywordsSIGNALING PROTEIN / Cell growth / GTPase activating protein / GTPase / coatomer complex
Function / homology
Function and homology information


MTOR signalling / GATOR1 complex / Gtr1-Gtr2 GTPase complex / GATOR2 complex / pseudohyphal growth / urea transport / negative regulation of small GTPase mediated signal transduction / protein localization to vacuole / Ragulator complex / microautophagy ...MTOR signalling / GATOR1 complex / Gtr1-Gtr2 GTPase complex / GATOR2 complex / pseudohyphal growth / urea transport / negative regulation of small GTPase mediated signal transduction / protein localization to vacuole / Ragulator complex / microautophagy / protein localization to vacuolar membrane / Seh1-associated complex / COPII-coated vesicle budding / nuclear pore localization / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / regulation of TORC1 signaling / Amino acids regulate mTORC1 / proline transport / nuclear pore outer ring / positive regulation of ER to Golgi vesicle-mediated transport / COPII vesicle coat / phosphate ion transport / positive regulation of protein exit from endoplasmic reticulum / fungal-type vacuole / regulation of autophagosome assembly / structural constituent of nuclear pore / endocytic recycling / vacuolar acidification / negative regulation of TOR signaling / fungal-type vacuole membrane / cellular response to nitrogen starvation / vacuolar membrane / nucleocytoplasmic transport / TORC1 signaling / regulation of receptor recycling / positive regulation of macroautophagy / endoplasmic reticulum exit site / nuclear pore / subtelomeric heterochromatin formation / transcription by RNA polymerase III / positive regulation of TOR signaling / mRNA transport / negative regulation of TORC1 signaling / transcription by RNA polymerase I / ERAD pathway / positive regulation of TORC1 signaling / signaling adaptor activity / positive regulation of autophagy / negative regulation of autophagy / cellular response to amino acid starvation / cellular response to starvation / cellular response to amino acid stimulus / GTPase activator activity / cell periphery / protein import into nucleus / meiotic cell cycle / late endosome / nuclear envelope / late endosome membrane / protein transport / nuclear membrane / cellular response to oxidative stress / 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 / positive regulation of DNA-templated transcription / endoplasmic reticulum membrane / chromatin / GTP binding / structural molecule activity / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family ...YNR034W-A/EGO2 / YNR034W-A/EGO2 superfamily / YNR034W-A-like / GSE/EGO complex subunit Slm4 / Protein SLM4 / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid / : / : / 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, vWA-like 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 / RagC/D / RWD domain / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / RWD domain profile. / RWD / RWD domain / Sec13/Seh1 family / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Zinc finger RING-type profile. / Zinc finger, RING-type / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / 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 / SEH-associated protein 4 / Protein SLM4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / Nucleoporin SEH1 / GTP-binding protein GTR2 / GTP-binding protein GTR1 ...ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / SEH-associated protein 4 / Protein SLM4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / Nucleoporin SEH1 / GTP-binding protein GTR2 / GTP-binding protein GTR1 / Protein MEH1 / Maintenance of telomere capping protein 5 / Protein transport protein SEC13 / Restriction of telomere capping protein 1 / Protein EGO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 22, 2024Deposition site: PDBE / Processing site: PDBE
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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
H: Protein transport protein SEC13
A: Restriction of telomere capping protein 1
F: Nucleoporin SEH1
E: Nucleoporin SEH1
G: SEH-associated protein 4
B: SEH-associated protein 4
D: Nucleoporin SEH1
K: Maintenance of telomere capping protein 5
P: Protein transport protein SEC13
I: Restriction of telomere capping protein 1
N: Nucleoporin SEH1
M: Nucleoporin SEH1
O: SEH-associated protein 4
J: SEH-associated protein 4
L: Nucleoporin SEH1
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
b: GTP-binding protein GTR1
d: GTP-binding protein GTR2
g: Nitrogen permease regulator 2
i: Nitrogen permease regulator 3
j: Vacuolar membrane-associated protein IML1
S: Protein MEH1
W: Protein EGO2
Z: Protein SLM4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,344,49268
Polymers2,340,67132
Non-polymers3,82136
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 , 9 types, 24 molecules CKHPAIFEDNMLGBOJXjRSUWYZ

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


Mass: 131104.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03897
#2: Protein Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04491
#3: Protein Restriction of telomere capping protein 1 / SEH-associated protein 2


Mass: 149533.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08281
#4: Protein
Nucleoporin SEH1 / Nuclear pore protein SEH1 / SEC13 homolog 1


Mass: 39170.758 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53011
#5: Protein
SEH-associated protein 4


Mass: 117775.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38164
#10: Protein Vacuolar membrane-associated protein IML1 / Increased minichromosome loss protein 1 / SEH-associated protein 1


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


Mass: 20266.086 Da / Num. of mol.: 2
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
#12: Protein Protein EGO2


Mass: 8104.935 Da / Num. of mol.: 2
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
#13: Protein Protein SLM4 / EGO complex subunit 3 / GSE complex subunit 1


Mass: 18371.877 Da / Num. of mol.: 2
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, 4 molecules abcd

#6: Protein GTP-binding protein GTR1


Mass: 35892.465 Da / Num. of mol.: 2
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
#7: Protein GTP-binding protein GTR2


Mass: 38633.961 Da / Num. of mol.: 2
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, 4 molecules Tghi

#8: Protein Nitrogen permease regulator 2


Mass: 69937.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39923
#9: Protein Nitrogen permease regulator 3 / Required for meiotic nuclear division protein 11


Mass: 130141.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38742

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Non-polymers , 4 types, 36 molecules

#14: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / 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-#130NATURAL
2SEA complexCOMPLEX#1-#3, #5, #4, #8-#101NATURAL
3EGO complexCOMPLEX#6-#7, #11-#131RECOMBINANT
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
19PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208039 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18adl

8adl

18adl1PDBexperimental model
21AlphaFoldin silico model
36jwp

6jwp

16jwp3PDBexperimental model

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