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- PDB-7nsb: Supramolecular assembly module of yeast Chelator-GID SR4 E3 ubiqu... -

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Basic information

Entry
Database: PDB / ID: 7nsb
TitleSupramolecular assembly module of yeast Chelator-GID SR4 E3 ubiquitin ligase
Components
  • Glucose-induced degradation protein 7
  • Glucose-induced degradation protein 8
  • Vacuolar import and degradation protein 30
KeywordsLIGASE / GID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM
Function / homology
Function and homology information


GID complex / traversing start control point of mitotic cell cycle / regulation of nitrogen utilization / negative regulation of gluconeogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / cell cycle / nucleus / cytoplasm
Similarity search - Function
Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / : / LIS1 homology (LisH) motif profile. ...Ran-binding protein Vid30/RanBPM/SPLA, SPRY domain / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / 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 / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Glucose-induced degradation protein 7 / Glucose-induced degradation protein 8 / Vacuolar import and degradation protein 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChrustowicz, J. / Sherpa, D. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 2items
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, C.R. / Hehl, L.A. / Gottemukkala, K.V. / Hansen, F.M. / Karayel, O. / Prabu, J.R. / Mann, M. / Alpi, A.F. / Schulman, B.A.
History
DepositionMar 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 26, 2021Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.3Jun 9, 2021Group: Derived calculations / Category: struct_conf
Revision 1.4Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
a: Vacuolar import and degradation protein 30
g: Glucose-induced degradation protein 7
7: Glucose-induced degradation protein 7
h: Glucose-induced degradation protein 8


Theoretical massNumber of molelcules
Total (without water)333,3064
Polymers333,3064
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17660 Å2
ΔGint-132 kcal/mol
Surface area83110 Å2
MethodPISA

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Components

#1: Protein Vacuolar import and degradation protein 30 / Glucose-induced degradation protein 1


Mass: 108287.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: VID30, GID1, YGL227W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53076
#2: Protein Glucose-induced degradation protein 7


Mass: 84607.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GID7, MOH2, YCL039W, YCL311, YCL39W / Production host: Escherichia coli (E. coli) / References: UniProt: P25569
#3: Protein Glucose-induced degradation protein 8 / Dosage-dependent cell cycle regulator 1


Mass: 55803.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GID8, DCR1, YMR135C, YM9375.04C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40208

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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: Supramolecular assembly module of yeast Chelator-GID SR4 comprising Gid1, Gid8 and a homodimer of Gid7
Type: COMPLEX
Details: Generated by focused refinement of Chelator-GID SR4 + Fbp1 map
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.33 MDa
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 79.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48629 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413774
ELECTRON MICROSCOPYf_angle_d0.6718754
ELECTRON MICROSCOPYf_dihedral_angle_d17.9411881
ELECTRON MICROSCOPYf_chiral_restr0.0452200
ELECTRON MICROSCOPYf_plane_restr0.0052361

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