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- EMDB-51904: Cryo-EM structure of the SEAC-EGOC supercomplex (consensus map) -

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Basic information

Entry
Database: EMDB / ID: EMD-51904
TitleCryo-EM structure of the SEAC-EGOC supercomplex (consensus map)
Map dataDeepEMhancer sharpened map
Sample
  • Complex: SEAC-EGOC supercomplex
    • Complex: SEA complex
    • Complex: EGO complex
KeywordsCell growth / GTPase activating protein / GTPase / coatomer complex / SIGNALING PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTafur L / Loewith R
Funding supportEuropean Union, 1 items
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 25, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51904.png

Downloads & links

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Map

FileDownload / File: emd_51904.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 512 pix.
= 522.701 Å		1.02 Å/pix.
x 512 pix.
= 522.701 Å		1.02 Å/pix.
x 512 pix.
= 522.701 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0209 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0508
Minimum - Maximum-0.0017250242 - 2.026677
Average (Standard dev.)0.0009805853 (±0.021660933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 522.7008 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51904_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_51904_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51904_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51904_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SEAC-EGOC supercomplex

EntireName: SEAC-EGOC supercomplex
Components
  • Complex: SEAC-EGOC supercomplex
    • Complex: SEA complex
    • Complex: EGO complex

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Supramolecule #1: SEAC-EGOC supercomplex

SupramoleculeName: SEAC-EGOC supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13

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Supramolecule #2: SEA complex

SupramoleculeName: SEA complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #8-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: EGO complex

SupramoleculeName: EGO complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7, #11-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 208039
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial model
PDB IDChain

8adl

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model

6jwp

source_name: PDB, initial_model_type: experimental model

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