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- EMDB-12557: Structure of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12557
TitleStructure of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to its tetrameric metabolic enzyme substrate Fbp1
Map data
SampleSupramolecular assembly of yeast GID complex comprising Gid1-Gid8-Gid2-Gid9-Gid5-Gid4-Gid7 bound to Fbp1 tetramer
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.34 Å
AuthorsChrustowicz J / Sherpa D / Prabu JR / Schulman BA
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Citation
Journal: Mol Cell / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme.
Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / ...Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / Matthias Mann / Arno F Alpi / Brenda A Schulman /
Abstract: How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of ...How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GID, which resembles an organometallic supramolecular chelate. The Chelator-GID assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.
#1: Journal: Biorxiv / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme
Authors: Sherpa D / Chrustowicz J / Qiao S / Langlois CR / Hehl LA / Gottemukkala KV / Hansen FM / Karayel O / Prabu JR / Mann M / Alpi AF / Schulman BA
History
DepositionMar 5, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 16, 2021-
Current statusJun 16, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0143
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0143
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_12557.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 288 pix.
= 455.04 Å
1.58 Å/pix.
x 288 pix.
= 455.04 Å
1.58 Å/pix.
x 288 pix.
= 455.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density
Contour LevelBy AUTHOR: 0.0143 / Movie #1: 0.0143
Minimum - Maximum-0.006449241 - 0.038378265
Average (Standard dev.)0.0008099908 (±0.003922898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 455.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.581.581.58
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z455.040455.040455.040
α/β/γ90.00090.00090.000
start NX/NY/NZ696888
NX/NY/NZ828048
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0060.0380.001

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Supplemental data

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Segmentation: #1

Fileemd_12557_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_12557_additional_1.map
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Half map: #2

Fileemd_12557_half_map_1.map
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Half map: #1

Fileemd_12557_half_map_2.map
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Sample components

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Entire Supramolecular assembly of yeast GID complex comprising Gid1-Gid8...

EntireName: Supramolecular assembly of yeast GID complex comprising Gid1-Gid8-Gid2-Gid9-Gid5-Gid4-Gid7 bound to Fbp1 tetramer
Number of components: 1

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Component #1: protein, Supramolecular assembly of yeast GID complex comprising ...

ProteinName: Supramolecular assembly of yeast GID complex comprising Gid1-Gid8-Gid2-Gid9-Gid5-Gid4-Gid7 bound to Fbp1 tetramer
Recombinant expression: No
MassTheoretical: 1.6 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 79.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2回回転対称) / Number of projections: 8328
3D reconstructionResolution: 10.34 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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