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- PDB-7ns4: Catalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 7ns4
TitleCatalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase
Components
  • E3 ubiquitin-protein ligase RMD5
  • Protein FYV10
KeywordsLIGASE / GID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM
Function / homology
Function and homology information


GID complex / Regulation of pyruvate metabolism / negative regulation of gluconeogenesis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / peroxisome / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of apoptotic process ...GID complex / Regulation of pyruvate metabolism / negative regulation of gluconeogenesis / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / peroxisome / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / negative regulation of apoptotic process / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Rmd5, degenerated RING (dRING) finger / Fyv10 family / Gid-type RING finger domain / Gid-type RING finger profile. / 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. / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Protein FYV10 / E3 ubiquitin-protein ligase RMD5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSherpa, D. / Chrustowicz, J. / 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 / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 9, 2021Group: Derived calculations / Category: struct_conf
Revision 1.3Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_admin
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

Deposited unit
b: E3 ubiquitin-protein ligase RMD5
i: Protein FYV10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3514
Polymers109,2202
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12890 Å2
ΔGint-158 kcal/mol
Surface area36150 Å2

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Components

#1: Protein E3 ubiquitin-protein ligase RMD5 / Glucose-induced degradation protein 2 / Required for meiotic nuclear division protein 5 / ...Glucose-induced degradation protein 2 / Required for meiotic nuclear division protein 5 / Sporulation protein RMD5


Mass: 49244.594 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: RMD5, GID2, YDR255C, YD9320A.05c / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q12508, RING-type E3 ubiquitin transferase
#2: Protein Protein FYV10 / Function required for yeast viability protein 10 / Glucose-induced degradation protein 9 / Probable ...Function required for yeast viability protein 10 / Glucose-induced degradation protein 9 / Probable E3 ubiquitin-protein ligase GID9


Mass: 59975.102 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: FYV10, GID9, YIL097W / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P40492, RING-type E3 ubiquitin transferase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: Catalytic module of yeast Chelator-GID SR4 comprising Gid2 and Gid9
Type: COMPLEX
Details: Generated by focused refinement of Chelator-GID SR4 + Fbp1 map
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.11 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 FIELD
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74254 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0065576
ELECTRON MICROSCOPYf_angle_d0.7797550
ELECTRON MICROSCOPYf_dihedral_angle_d14.508726
ELECTRON MICROSCOPYf_chiral_restr0.048888
ELECTRON MICROSCOPYf_plane_restr0.004936

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