[English] 日本語
Yorodumi
- PDB-9h5k: Cryo-EM structure of the SEAC-EGOC supercomplex -

+
Open data


ID or keywords:

Loading...

-
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 / pseudohyphal growth / GATOR2 complex / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / positive regulation of ER to Golgi vesicle-mediated transport / Ragulator complex / microautophagy ...MTOR signalling / GATOR1 complex / pseudohyphal growth / GATOR2 complex / Gtr1-Gtr2 GTPase complex / urea transport / negative regulation of small GTPase mediated signal transduction / positive regulation of ER to Golgi vesicle-mediated transport / Ragulator complex / microautophagy / protein localization to vacuolar membrane / protein localization to vacuole / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / Amino acids regulate mTORC1 / proline transport / COPII-mediated vesicle transport / regulation of TORC1 signaling / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / COPII vesicle coat / Regulation of HSF1-mediated heat shock response / phosphate ion transport / regulation of autophagosome assembly / TORC1 signaling / SUMOylation of SUMOylation proteins / fungal-type vacuole / endocytic recycling / structural constituent of nuclear pore / vacuolar acidification / fungal-type vacuole membrane / SUMOylation of RNA binding proteins / negative regulation of TOR signaling / SUMOylation of chromatin organization proteins / cellular response to nitrogen starvation / vacuolar membrane / nucleocytoplasmic transport / transcription by RNA polymerase III / positive regulation of macroautophagy / regulation of receptor recycling / positive regulation of TOR signaling / mRNA transport / nuclear pore / subtelomeric heterochromatin formation / transcription by RNA polymerase I / negative regulation of TORC1 signaling / ERAD pathway / 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 / cell periphery / meiotic cell cycle / cellular response to amino acid stimulus / protein import into nucleus / late endosome membrane / nuclear envelope / late endosome / protein transport / cellular response to oxidative stress / nuclear membrane / 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 / endoplasmic reticulum membrane / chromatin / GTP binding / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / 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 / 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 / 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 / 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 / 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 / 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: 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 22, 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: Additional map / Part number: 6 / Data content type: Additional 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more