6SWY

Structure of active GID E3 ubiquitin ligase complex minus Gid2 and delta Gid9 RING domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history


Literature

Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly

Qiao, S.Langlois, C.R.Chrustowicz, J.Sherpa, D.Karayel, O.Hansen, F.M.Beier, V.von Gronau, S.Bollschweiler, D.Schafer, T.Alpi, A.F.Mann, M.Rajan Prabu, J.Schulman, B.A.

(2020) Mol Cell 77: 1-14

  • DOI: https://doi.org/10.1016/j.molcel.2019.10.009
  • Primary Citation of Related Structures:  
    6SWY

  • PubMed 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 gluconeogenesis is terminated upon glucose availability, a process that involves the multiprotein E3 ligase GID SR4 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 Ant ), which awaits a glucose-induced substrate receptor to form the active GID SR4 . Meanwhile, other environmental perturbations elicit production of an alternative substrate receptor assembling into a related E3 ligase complex. The intricate structure of GID Ant enables anticipating and ultimately binding various N-degron-targeting (i.e., "N-end rule") substrate receptors, while the GID SR4 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.


  • Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar import and degradation protein 28A [auth 5]921Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VID28GID5YIL017C
UniProt
Find proteins for P40547 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P40547
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40547
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-induced degradation protein 8B [auth 8]455Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GID8DCR1YMR135CYM9375.04C
UniProt
Find proteins for P40208 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40208
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30,Vacuolar import and degradation protein 30C [auth 1]1,064Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VID30GID1YGL227W
UniProt
Find proteins for P53076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53076
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar import and degradation protein 24D [auth 4]362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VID24GID4YBR105CYBR0834
UniProt
Find proteins for P38263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38263
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10,Protein FYV10E [auth 9]479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FYV10GID9YIL097W
EC: 2.3.2.27
UniProt
Find proteins for P40492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40492
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 2.0: 2022-07-20
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-07-10
    Changes: Data collection