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- EMDB-51905: Cryo-EM structure of the SEAC-EGOC supercomplex (monomer focused map) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51905
TitleCryo-EM structure of the SEAC-EGOC supercomplex (monomer focused 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: 3.0 Å
AuthorsTafur L / Loewith R
Funding supportEuropean Union, 1 items
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 25, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51905.png

Downloads & links

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Map

FileDownload / File: emd_51905.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: 0.0507
Minimum - Maximum-0.001758555 - 2.0211184
Average (Standard dev.)0.00038042248 (±0.014292078)
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_51905_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_51905_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_51905_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_51905_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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: C2-symmetry expanded, signal subtracted particles / Number images used: 416078
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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