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- EMDB-14323: Structure of Chelator-GIDSR4 bound to Mdh2 -

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Basic information

Entry
Database: EMDB / ID: EMD-14323
TitleStructure of Chelator-GIDSR4 bound to Mdh2
Map data
Sample
  • Complex: Gid1, Gid2, Gid4, Gid5, Gid7, Gid8, Gid9, Mdh2
Keywordsmultiprotein complex / E3 ligase / metabolic enzyme / LIGASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.9 Å
AuthorsSherpa D / Chrustowicz J / Schulman B
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation.
Authors: Shuai Qiao / Chia-Wei Lee / Dawafuti Sherpa / Jakub Chrustowicz / Jingdong Cheng / Maximilian Duennebacke / Barbara Steigenberger / Ozge Karayel / Duc Tung Vu / Susanne von Gronau / Matthias ...Authors: Shuai Qiao / Chia-Wei Lee / Dawafuti Sherpa / Jakub Chrustowicz / Jingdong Cheng / Maximilian Duennebacke / Barbara Steigenberger / Ozge Karayel / Duc Tung Vu / Susanne von Gronau / Matthias Mann / Florian Wilfling / Brenda A Schulman /
Abstract: Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced ...Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced degradation of fructose-1,6-bisphosphatase (Fbp1), malate dehydrogenase (Mdh2), and other gluconeogenic enzymes. "GID" is a collection of E3 ligase complexes; a core scaffold, RING-type catalytic core, and a supramolecular assembly module together with interchangeable substrate receptors select targets for ubiquitylation. However, knowledge of additional cellular factors directly regulating GID-type E3s remains rudimentary. Here, we structurally and biochemically characterize Gid12 as a modulator of the GID E3 ligase complex. Our collection of cryo-EM reconstructions shows that Gid12 forms an extensive interface sealing the substrate receptor Gid4 onto the scaffold, and remodeling the degron binding site. Gid12 also sterically blocks a recruited Fbp1 or Mdh2 from the ubiquitylation active sites. Our analysis of the role of Gid12 establishes principles that may more generally underlie E3 ligase regulation.
History
DepositionFeb 10, 2022-
Header (metadata) releaseJun 8, 2022-
Map releaseJun 8, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14323.png

Downloads & links

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Map

FileDownload / File: emd_14323.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.77 Å/pix.
x 120 pix.
= 452.4 Å		3.77 Å/pix.
x 120 pix.
= 452.4 Å		3.77 Å/pix.
x 120 pix.
= 452.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0414
Minimum - Maximum-0.040616095 - 0.13963783
Average (Standard dev.)0.0021985713 (±0.011404834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 452.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14323_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14323_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14323_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Gid1, Gid2, Gid4, Gid5, Gid7, Gid8, Gid9, Mdh2

EntireName: Gid1, Gid2, Gid4, Gid5, Gid7, Gid8, Gid9, Mdh2
Components
  • Complex: Gid1, Gid2, Gid4, Gid5, Gid7, Gid8, Gid9, Mdh2

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Supramolecule #1: Gid1, Gid2, Gid4, Gid5, Gid7, Gid8, Gid9, Mdh2

SupramoleculeName: Gid1, Gid2, Gid4, Gid5, Gid7, Gid8, Gid9, Mdh2 / type: complex / ID: 1 / Parent: 0
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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.8 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

12541

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23114
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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