2DYM

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Atg5.Atg16, a complex essential for autophagy

Matsushita, M.Suzuki, N.N.Obara, K.Fujioka, Y.Ohsumi, Y.Inagaki, F.

(2007) J.Biol.Chem. 282: 6763-6772

  • DOI: 10.1074/jbc.M609876200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Atg5 is covalently modified with a ubiquitin-like modifier, Atg12, and the Atg12-Atg5 conjugate further forms a complex with the multimeric protein Atg16. The Atg12-Atg5.Atg16 multimeric complex plays an essential role in autophagy, the bulk degradat ...

    Atg5 is covalently modified with a ubiquitin-like modifier, Atg12, and the Atg12-Atg5 conjugate further forms a complex with the multimeric protein Atg16. The Atg12-Atg5.Atg16 multimeric complex plays an essential role in autophagy, the bulk degradation system conserved in all eukaryotes. We have reported here the crystal structure of Atg5 complexed with the N-terminal region of Atg16 at 1.97A resolution. Atg5 comprises two ubiquitin-like domains that flank a helix-rich domain. The N-terminal region of Atg16 has a helical structure and is bound to the groove formed by these three domains. In vitro analysis showed that Arg-35 and Phe-46 of Atg16 are crucial for the interaction. Atg16, with a mutation at these residues, failed to localize to the pre-autophagosomal structure and could not restore autophagy in Atg16-deficient yeast strains. Furthermore, these Atg16 mutants could not restore a severe reduction in the formation of the Atg8-phosphatidylethanolamine conjugate, another essential factor for autophagy, in Atg16-deficient strains under starvation conditions. These results taken together suggest that the direct interaction between Atg5 and Atg16 is crucial to the performance of their roles in autophagy.


    Related Citations: 
    • Expression, purification and crystallization of the Atg5-Atg16 complex essential for autophagy
      Matsushita, M.,Suzuki, N.N.,Fujioka, Y.,Ohsumi, Y.,Inagaki, F.
      (2006) Acta Crystallogr.,Sect.F 62: 1021


    Organizational Affiliation

    Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-21, W-11, Kita-ku, Sapporo 001-0021, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Autophagy protein 5
A, C, E, G
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATG5 (APG5)
Find proteins for Q12380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ATG5
Go to UniProtKB:  Q12380
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy protein 16
B, D, F, H
46Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATG16 (APG15, APG16, CVT11, SAP18)
Find proteins for Q03818 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03818
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.347α = 90.00
b = 104.417β = 92.11
c = 112.153γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance