6WY6

Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits.

Wilfling, F.Lee, C.W.Erdmann, P.S.Zheng, Y.Sherpa, D.Jentsch, S.Pfander, B.Schulman, B.A.Baumeister, W.

(2020) Mol Cell 80: 764

  • DOI: https://doi.org/10.1016/j.molcel.2020.10.030
  • Primary Citation of Related Structures:  
    6WY6

  • PubMed Abstract: 

    Autophagy eliminates cytoplasmic content selected by autophagy receptors, which link cargo to the membrane-bound autophagosomal ubiquitin-like protein Atg8/LC3. Here, we report a selective autophagy pathway for protein condensates formed by endocytic proteins in yeast. In this pathway, the endocytic protein Ede1 functions as a selective autophagy receptor. Distinct domains within Ede1 bind Atg8 and mediate phase separation into condensates. Both properties are necessary for an Ede1-dependent autophagy pathway for endocytic proteins, which differs from regular endocytosis and does not involve other known selective autophagy receptors but requires the core autophagy machinery. Cryo-electron tomography of Ede1-containing condensates, at the plasma membrane and in autophagic bodies, shows a phase-separated compartment at the beginning and end of the Ede1-mediated selective autophagy route. Our data suggest a model for autophagic degradation of macromolecular protein complexes by the action of intrinsic autophagy receptors.


  • Organizational Affiliation

    Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. Electronic address: fwilfling@biochem.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 8A [auth B],
B [auth A]
118Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: ATG8APG8AUT7CVT5SCY_0144
UniProt
Find proteins for P38182 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38182 
Go to UniProtKB:  P38182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38182
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EH domain-containing and endocytosis protein 1
C, D
28Saccharomyces cerevisiaeMutation(s): 1 
UniProt
Find proteins for P34216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34216 
Go to UniProtKB:  P34216
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34216
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
C, D
L-PEPTIDE LINKINGC5 H9 N O3ALA
XSN
Query on XSN
C, D
L-PEPTIDE LINKINGC4 H8 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.642α = 90
b = 49.642β = 90
c = 123.446γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Max Planck SocietyGermany--
European Research Council (ERC)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description