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- PDB-7wug: GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module -

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Basic information

Entry
Database: PDB / ID: 7wug
TitleGID subcomplex: Gid12 bound Substrate Receptor Scaffolding module
Components
  • Glucose-induced degradation protein 8
  • HLJ1_G0042170.mRNA.1.CDS.1
  • Vacuolar import and degradation protein 24
  • Vacuolar import and degradation protein 28
  • Vacuolar import and degradation protein 30
KeywordsLIGASE / E3 ubiquitin Ligase / beta-propellor
Function / homology
Function and homology information


protein catabolic process in the vacuole / GID complex / ascospore formation / traversing start control point of mitotic cell cycle / vacuole / negative regulation of gluconeogenesis / Neutrophil degranulation / proteasome-mediated ubiquitin-dependent protein catabolic process / cell cycle / nucleus / cytoplasm
Similarity search - Function
Armadillo-type fold containing protein ARMC8/Vid28 / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. ...Armadillo-type fold containing protein ARMC8/Vid28 / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / Vacuolar import/degradation protein Vid24 / Vacuolar import and degradation protein / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / LIS1 homology (LisH) motif profile. / LIS1 homology motif / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / Domain in SPla and the RYanodine Receptor. / Armadillo-like helical / Concanavalin A-like lectin/glucanase domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
YDL176W isoform 1 / Vacuolar import and degradation protein 24 / BJ4_G0038950.mRNA.1.CDS.1 / Glucose-induced degradation protein 8 / Vacuolar import and degradation protein 28
Similarity search - Component
Biological speciesSaccharomyces cerevisiae YJM1133 (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsQiao, S. / Cheng, J.D. / Schulman, B.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
Citation
Journal: 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.
#1: Journal: Mol Cell / 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, C.R. / Hehl, L.A. / Gottemukkala, K.V. / Hansen, F.M. / Karayel, O. / von Gronau, S. / Prabu, J.R. / Mann, M. / Alpi, A.F. / Schulman, B.A.
History
DepositionFeb 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
5: Vacuolar import and degradation protein 28
8: Glucose-induced degradation protein 8
1: Vacuolar import and degradation protein 30
4: Vacuolar import and degradation protein 24
Y: HLJ1_G0042170.mRNA.1.CDS.1


Theoretical massNumber of molelcules
Total (without water)388,5925
Polymers388,5925
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Vacuolar import and degradation protein 28 / Glucose-induced degradation protein 5


Mass: 105658.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae YJM1133 (yeast)
Strain: ATCC 204508 / S288c / Gene: VID28, GID5, YIL017C
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P40547
#2: Protein Glucose-induced degradation protein 8 / Dosage-dependent cell cycle regulator 1


Mass: 51789.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GID8, DCR1, YMR135C, YM9375.04C
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: P40208
#3: Protein Vacuolar import and degradation protein 30


Mass: 108287.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCNYR20_0003002900, SCP684_0002002900
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6L0ZCH7
#4: Protein Vacuolar import and degradation protein 24


Mass: 41291.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCP684_0007018400
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6A5Q1W0
#5: Protein HLJ1_G0042170.mRNA.1.CDS.1 / Uncharacterized protein YDL176W / Y55_G0042020.mRNA.1.CDS.1


Mass: 81564.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS770, PACBIOSEQ_LOCUS781, SCNYR20_0001006100, SCP684_0001006100
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A6A5Q188

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gid12-SRS / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.392 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 6.5 / Details: 25mM MES pH6.5 + 500mM NaCl + 1mM DTT
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 39 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.335 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198503 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417873
ELECTRON MICROSCOPYf_angle_d0.66224227
ELECTRON MICROSCOPYf_dihedral_angle_d4.492383
ELECTRON MICROSCOPYf_chiral_restr0.0452795
ELECTRON MICROSCOPYf_plane_restr0.0053049

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