7QQY | pdb_00007qqy

yeast Gid10 bound to Art2 Pro/N-degron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 
    0.227 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QQY

This is version 1.3 of the entry. See complete history

Literature

A GID E3 ligase assembly ubiquitinates an Rsp5 E3 adaptor and regulates plasma membrane transporters.

Langlois, C.R.Beier, V.Karayel, O.Chrustowicz, J.Sherpa, D.Mann, M.Schulman, B.A.

(2022) EMBO Rep 23: e53835-e53835

  • DOI: https://doi.org/10.15252/embr.202153835
  • Primary Citation Related Structures: 
    7QQY

  • PubMed Abstract: 

    Cells rapidly remodel their proteomes to align their cellular metabolism to environmental conditions. Ubiquitin E3 ligases enable this response, by facilitating rapid and reversible changes to protein stability, localization, or interaction partners. In Saccharomyces cerevisiae, the GID E3 ligase regulates the switch from gluconeogenic to glycolytic conditions through induction and incorporation of the substrate receptor subunit Gid4, which promotes the degradation of gluconeogenic enzymes. Here, we show an alternative substrate receptor, Gid10, which is induced in response to changes in temperature, osmolarity, and nutrient availability, regulates the ART-Rsp5 ubiquitin ligase pathway, a component of plasma membrane quality control. Proteomic studies reveal that the levels of the adaptor protein Art2 are elevated upon GID10 deletion. A crystal structure shows the basis for Gid10-Art2 interactions, and we demonstrate that Gid10 directs a GID E3 ligase complex to ubiquitinate Art2. Our data suggest that the GID E3 ligase affects Art2-dependent amino acid transport. This study reveals GID as a system of E3 ligases with metabolic regulatory functions outside of glycolysis and gluconeogenesis, controlled by distinct stress-specific substrate receptors.


  • Organizational Affiliation
    • Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 27.23 kDa 
  • Atom Count: 2,072 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 232 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein YGR066C224Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YGR066C
UniProt
Find proteins for P53242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53242 
Go to UniProtKB:  P53242
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53242
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ECM218Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38167 
Go to UniProtKB:  P38167
Entity Groups
UniProt GroupP38167
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.524α = 90
b = 67.817β = 90
c = 75.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)European UnionSCHU 3196/1
European Research Council (ERC)European Union789016-NEDD8Activate

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2022-06-15
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description