9H5K | pdb_00009h5k

Cryo-EM structure of the SEAC-EGOC supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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Literature

Structure and function of the yeast amino acid-sensing SEAC-EGOC supercomplex.

Tafur, L.Bonadei, L.Zheng, Y.Gabus, C.Loewith, R.

(2026) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-026-01746-2
  • Primary Citation of Related Structures:  
    9H4Q, 9H5K

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland. ltafur@cnio.es.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maintenance of telomere capping protein 5A [auth C],
I [auth K]
1,148Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein SEC13B [auth H],
J [auth P]
297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Restriction of telomere capping protein 1C [auth A],
K [auth I]
1,341Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupQ08281
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin SEH1349Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SEH-associated protein 4F [auth G],
G [auth B],
N [auth O],
O [auth J]
1,038Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein GTR1Q [auth a],
Y [auth b]
310Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GTR1YML121WYM7056.05
EC: 3.6.5
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein GTR2R [auth c],
Z [auth d]
341Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: GTR2YGR163W
EC: 3.6.5
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogen permease regulator 2AA [auth g],
S [auth T]
615Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogen permease regulator 3BA [auth i],
T [auth h]
1,146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar membrane-associated protein IML1CA [auth j],
U [auth X]
1,584Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MEH1DA [auth S],
V [auth R]
184Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MEH1EGO1GSE2YKR007WYK106
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Protein EGO2EA [auth W],
W [auth U]
75Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: EGO2YCR075W-A
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SLM4FA [auth Z],
X [auth Y]
162Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLM4EGO3GSE1YBR077CYBR0723
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

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KB [auth a],
LB [auth c],
OB [auth b],
PB [auth d]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
AF3 (Subject of Investigation/LOI)
Query on AF3

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JB [auth a],
NB [auth b]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
ZN (Subject of Investigation/LOI)
Query on ZN

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AB [auth O]
BB [auth O]
CB [auth O]
DB [auth O]
EB [auth J]
AB [auth O],
BB [auth O],
CB [auth O],
DB [auth O],
EB [auth J],
FB [auth J],
GA [auth C],
GB [auth J],
HA [auth C],
HB [auth J],
IA [auth C],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth G],
NA [auth G],
OA [auth G],
PA [auth G],
QA [auth B],
RA [auth B],
SA [auth B],
TA [auth B],
UA [auth K],
VA [auth K],
WA [auth K],
XA [auth I],
YA [auth I],
ZA [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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IB [auth a],
MB [auth b]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionAdG TENDO

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2026-03-04
    Changes: Data collection, Database references