3VXW

Crystal structure of Saccharomyces cerevisiae Atg8 complexed with Atg32 AIM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Autophagy-related protein 32 acts as autophagic degron and directly initiates mitophagy

Kondo-Okamoto, N.Noda, N.N.Suzuki, S.W.Nakatogawa, H.Takahashi, I.Matsunami, M.Hashimoto, A.Inagaki, F.Ohsumi, Y.Okamoto, K.

(2012) J Biol Chem 287: 10631-10638

  • DOI: https://doi.org/10.1074/jbc.M111.299917
  • Primary Citation of Related Structures:  
    3VXW

  • PubMed Abstract: 

    Autophagy-related degradation selective for mitochondria (mitophagy) is an evolutionarily conserved process that is thought to be critical for mitochondrial quality and quantity control. In budding yeast, autophagy-related protein 32 (Atg32) is inserted into the outer membrane of mitochondria with its N- and C-terminal domains exposed to the cytosol and mitochondrial intermembrane space, respectively, and plays an essential role in mitophagy. Atg32 interacts with Atg8, a ubiquitin-like protein localized to the autophagosome, and Atg11, a scaffold protein required for selective autophagy-related pathways, although the significance of these interactions remains elusive. In addition, whether Atg32 is the sole protein necessary and sufficient for initiation of autophagosome formation has not been addressed. Here we show that the Atg32 IMS domain is dispensable for mitophagy. Notably, when anchored to peroxisomes, the Atg32 cytosol domain promoted autophagy-dependent peroxisome degradation, suggesting that Atg32 contains a module compatible for other organelle autophagy. X-ray crystallography reveals that the Atg32 Atg8 family-interacting motif peptide binds Atg8 in a conserved manner. Mutations in this binding interface impair association of Atg32 with the free form of Atg8 and mitophagy. Moreover, Atg32 variants, which do not stably interact with Atg11, are strongly defective in mitochondrial degradation. Finally, we demonstrate that Atg32 forms a complex with Atg8 and Atg11 prior to and independent of isolation membrane generation and subsequent autophagosome formation. Taken together, our data implicate Atg32 as a bipartite platform recruiting Atg8 and Atg11 to the mitochondrial surface and forming an initiator complex crucial for mitophagy.


  • Organizational Affiliation

    Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 8119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: APG8ATG8AUT7CVT5YBL0732YBL078C
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:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Autophagy-related protein 326Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40458 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40458 
Go to UniProtKB:  P40458
Entity Groups  
UniProt GroupP40458
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.836α = 90
b = 104.836β = 90
c = 104.836γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description