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- PDB-7ns3: Substrate receptor scaffolding module of yeast Chelator-GID SR4 E... -

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Basic information

Entry
Database: PDB / ID: 7ns3
TitleSubstrate receptor scaffolding module of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to Fbp1 substrate
Components
  • (Vacuolar import and degradation protein ...) x 2
  • BJ4_G0018240.mRNA.1.CDS.1
  • Fructose-bisphosphatase
  • Glucose-induced degradation protein 8
  • Protein FYV10
KeywordsLIGASE / GID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM
Function / homology
Function and homology information


protein catabolic process in the vacuole / GID complex / ascospore formation / traversing start control point of mitotic cell cycle / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / vacuole / negative regulation of gluconeogenesis / Neutrophil degranulation / ubiquitin protein ligase activity ...protein catabolic process in the vacuole / GID complex / ascospore formation / traversing start control point of mitotic cell cycle / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / vacuole / negative regulation of gluconeogenesis / Neutrophil degranulation / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / carbohydrate metabolic process / cell cycle / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Protein Fyv10/E3 ubiquitin-protein transferase MAEA / Armadillo-type fold containing protein ARMC8/Vid28 / Gid-type RING finger domain / Gid-type RING finger profile. / 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 ...Protein Fyv10/E3 ubiquitin-protein transferase MAEA / Armadillo-type fold containing protein ARMC8/Vid28 / Gid-type RING finger domain / Gid-type RING finger profile. / 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. / Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain / 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
Fructose-bisphosphatase / Protein FYV10 / 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 (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 / 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
Item: _struct_sheet.id / _struct_sheet.number_strands
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
Revision 2.0Jul 7, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / em_software / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine_ls_restr / struct_conn
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_conn.pdbx_dist_value
Description: Model completeness
Details: We made a residue shift in a beta sheet starting residue K338 - L348 in the chain 4 (protein-Gid4)
Provider: author / Type: Coordinate replacement

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Structure visualization

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Assembly

Deposited unit
5: Vacuolar import and degradation protein 28
8: Glucose-induced degradation protein 8
1: BJ4_G0018240.mRNA.1.CDS.1
9: Protein FYV10
4: Vacuolar import and degradation protein 24
Fb: Fructose-bisphosphatase


Theoretical massNumber of molelcules
Total (without water)409,2716
Polymers409,2716
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area29470 Å2
ΔGint-205 kcal/mol
Surface area79880 Å2
MethodPISA

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Components

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Vacuolar import and degradation protein ... , 2 types, 2 molecules 54

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


Mass: 105609.133 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: VID28, GID5, YIL017C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40547
#5: 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: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q1W0

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Protein , 4 types, 4 molecules 819Fb

#2: 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
#3: Protein BJ4_G0018240.mRNA.1.CDS.1 / 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: PACBIOSEQ_LOCUS2437, SCNYR20_0003002900, SCP684_0002002900
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6L0ZCH7
#4: Protein Protein FYV10 / Protein fyv10


Mass: 59975.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS1661, PACBIOSEQ_LOCUS1718 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6A5PZU1
#6: Protein Fructose-bisphosphatase


Mass: 38303.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PACBIOSEQ_LOCUS4585, PACBIOSEQ_LOCUS4655, SCNYR20_0004037500, SCP684_0004037100
Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PV82, fructose-bisphosphatase

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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: Substrate receptor scaffolding module of yeast Chelator-GID SR4 comprising Gid1, Gid4, Gid5, Gid8 and Gid9 bound to Fbp1
Type: COMPLEX
Details: Generated by focused refinement of Chelator-GID SR4 + Fbp1 map
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.31 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74929 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414745
ELECTRON MICROSCOPYf_angle_d0.56220004
ELECTRON MICROSCOPYf_dihedral_angle_d18.7591958
ELECTRON MICROSCOPYf_chiral_restr0.0422331
ELECTRON MICROSCOPYf_plane_restr0.0042500

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