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- EMDB-10326: Structure of inactive GID E3 ubiquitin ligase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10326
TitleStructure of inactive GID E3 ubiquitin ligase complex
Map data
Sample
  • Complex: GIDAnt
Biological speciessaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQiao S / Prabu JR / Schulman BA
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2020
Title: Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly.
Authors: Shuai Qiao / Christine R Langlois / Jakub Chrustowicz / Dawafuti Sherpa / Ozge Karayel / Fynn M Hansen / Viola Beier / Susanne von Gronau / Daniel Bollschweiler / Tillman Schäfer / Arno F ...Authors: Shuai Qiao / Christine R Langlois / Jakub Chrustowicz / Dawafuti Sherpa / Ozge Karayel / Fynn M Hansen / Viola Beier / Susanne von Gronau / Daniel Bollschweiler / Tillman Schäfer / Arno F Alpi / Matthias Mann / J Rajan Prabu / Brenda A Schulman /
Abstract: Cells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, in Saccharomyces cerevisiae, carbon stress-induced ...Cells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, in Saccharomyces cerevisiae, carbon stress-induced gluconeogenesis is terminated upon glucose availability, a process that involves the multiprotein E3 ligase GID recruiting N termini and catalyzing ubiquitylation of gluconeogenic enzymes. Here, genetics, biochemistry, and cryoelectron microscopy define molecular underpinnings of glucose-induced degradation. Unexpectedly, carbon stress induces an inactive anticipatory complex (GID), which awaits a glucose-induced substrate receptor to form the active GID. Meanwhile, other environmental perturbations elicit production of an alternative substrate receptor assembling into a related E3 ligase complex. The intricate structure of GID enables anticipating and ultimately binding various N-degron-targeting (i.e., "N-end rule") substrate receptors, while the GID E3 forms a clamp-like structure juxtaposing substrate lysines with the ubiquitylation active site. The data reveal evolutionarily conserved GID complexes as a family of multisubunit E3 ubiquitin ligases responsive to extracellular stimuli.
History
DepositionSep 23, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 20, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10326.png

Downloads & links

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Map

FileDownload / File: emd_10326.map.gz / Format: CCP4 / Size: 83.7 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.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å		1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0135 / Movie #1: 0.0135
Minimum - Maximum-0.09237005 - 0.16481705
Average (Standard dev.)0.00031701045 (±0.003808567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.79996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z296.800296.800296.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0920.1650.000

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Supplemental data

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Mask #1

Fileemd_10326_msk_1.map
Projections & Slices
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Additional map: Multibody refinement of Gid2 9

Fileemd_10326_additional.map
AnnotationMultibody refinement of Gid2_9
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Additional map: Multibody refinement of Gid2 9

Fileemd_10326_additional_1.map
AnnotationMultibody refinement of Gid2_9
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Half map: #2

Fileemd_10326_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_10326_half_map_2.map
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Sample components

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Entire : GIDAnt

EntireName: GIDAnt
Components
  • Complex: GIDAnt

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Supramolecule #1: GIDAnt

SupramoleculeName: GIDAnt / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Molecular weightTheoretical: 374.44 KDa

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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

Concentration0.25 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
25.0 mMC6H13NO4SMES
1.0 mMC4H10O2S2DTT
500.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 10s and 10 f blot after 30s incubation time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 55.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER
Details: 3D initial model generated de novo from the 2D particles in relion suite
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 72130
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Details: empirical Bayesian approach
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Details: empirical Bayesian approach
FSC plot (resolution estimation)

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