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Yorodumi- EMDB-10331: Structure of endogenous inactive GID E3 ubiquitin ligase complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10331 | |||||||||
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Title | Structure of endogenous inactive GID E3 ubiquitin ligase complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.3 Å | |||||||||
Authors | Qiao S / Prabu JR / Schulman BA | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Mol Cell / Year: 2020 Title: Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly. Authors: Shuai Qiao / Christine R Langlois / Jakub Chrustowicz / Dawafuti Sherpa / Ozge Karayel / Fynn M Hansen / Viola Beier / Susanne von Gronau / Daniel Bollschweiler / Tillman Schäfer / Arno F ...Authors: Shuai Qiao / Christine R Langlois / Jakub Chrustowicz / Dawafuti Sherpa / Ozge Karayel / Fynn M Hansen / Viola Beier / Susanne von Gronau / Daniel Bollschweiler / Tillman Schäfer / Arno F Alpi / Matthias Mann / J Rajan Prabu / Brenda A Schulman / Abstract: Cells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, in Saccharomyces cerevisiae, carbon stress-induced ...Cells respond to environmental changes by toggling metabolic pathways, preparing for homeostasis, and anticipating future stresses. For example, in Saccharomyces cerevisiae, carbon stress-induced gluconeogenesis is terminated upon glucose availability, a process that involves the multiprotein E3 ligase GID recruiting N termini and catalyzing ubiquitylation of gluconeogenic enzymes. Here, genetics, biochemistry, and cryoelectron microscopy define molecular underpinnings of glucose-induced degradation. Unexpectedly, carbon stress induces an inactive anticipatory complex (GID), which awaits a glucose-induced substrate receptor to form the active GID. Meanwhile, other environmental perturbations elicit production of an alternative substrate receptor assembling into a related E3 ligase complex. The intricate structure of GID enables anticipating and ultimately binding various N-degron-targeting (i.e., "N-end rule") substrate receptors, while the GID E3 forms a clamp-like structure juxtaposing substrate lysines with the ubiquitylation active site. The data reveal evolutionarily conserved GID complexes as a family of multisubunit E3 ubiquitin ligases responsive to extracellular stimuli. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10331.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-10331-v30.xml emd-10331.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10331_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_10331.png | 52.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10331 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10331 | HTTPS FTP |
-Validation report
Summary document | emd_10331_validation.pdf.gz | 232.9 KB | Display | EMDB validaton report |
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Full document | emd_10331_full_validation.pdf.gz | 232.1 KB | Display | |
Data in XML | emd_10331_validation.xml.gz | 10.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10331 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10331 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10331.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.612 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Endogenous GIDAnt
Entire | Name: Endogenous GIDAnt |
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Components |
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-Supramolecule #1: Endogenous GIDAnt
Supramolecule | Name: Endogenous GIDAnt / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Recombinant expression | Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) |
Molecular weight | Theoretical: 374 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 67.2 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |