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- PDB-7ns3: Substrate receptor scaffolding module of yeast Chelator-GID SR4 E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ns3 | |||||||||
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Title | Substrate receptor scaffolding module of yeast Chelator-GID SR4 E3 ubiquitin ligase bound to Fbp1 substrate | |||||||||
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![]() | LIGASE / GID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM | |||||||||
Function / homology | ![]() protein catabolic process in the vacuole / GID complex / Regulation of pyruvate metabolism / 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 ...protein catabolic process in the vacuole / GID complex / Regulation of pyruvate metabolism / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Sherpa, D. / Chrustowicz, J. / Prabu, J.R. / Schulman, B.A. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 365.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12559MC ![]() 7ns4C ![]() 7ns5C ![]() 7nsbC ![]() 7nscC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Vacuolar import and degradation protein ... , 2 types, 2 molecules 54
#1: Protein | Mass: 105609.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: VID28, GID5, YIL017C / Production host: ![]() |
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#5: Protein | Mass: 41291.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SCP684_0007018400 / Production host: ![]() ![]() |
-Protein , 4 types, 4 molecules 819Fb
#2: Protein | Mass: 55803.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: GID8, DCR1, YMR135C, YM9375.04C / Production host: ![]() |
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#3: Protein | Mass: 108287.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS2437, SCNYR20_0003002900, SCP684_0002002900 Production host: ![]() |
#4: Protein | Mass: 59975.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS1661, PACBIOSEQ_LOCUS1718 / Production host: ![]() |
#6: Protein | Mass: 38303.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS4585, PACBIOSEQ_LOCUS4655, SCNYR20_0004037500, SCP684_0004037100 Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 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 |
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Molecular weight | Value: 0.31 MDa |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 79.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74929 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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