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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 / TORC1 signaling / endocytic recycling / vacuolar acidification / fungal-type vacuole membrane / negative regulation of TOR signaling / cellular response to nitrogen starvation / vacuolar membrane / 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 / signaling adaptor activity / positive regulation of TORC1 signaling / positive regulation of autophagy / 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 membrane / late endosome / 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 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / : / : / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1, N-terminal domain / DEPDC5 protein C-terminal region / GATOR1 complex protein NPRL3, C-terminal HTH / 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 / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding 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: To Be Published
Title: Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex
Authors: Tafur, L. / Bonadei, L. / Zheng, Y. / Loewith, R.
History
DepositionOct 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 5 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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