4P1N

Crystal structure of Atg1-Atg13 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural basis of starvation-induced assembly of the autophagy initiation complex.

Fujioka, Y.Suzuki, S.W.Yamamoto, H.Kondo-Kakuta, C.Kimura, Y.Hirano, H.Akada, R.Inagaki, F.Ohsumi, Y.Noda, N.N.

(2014) Nat Struct Mol Biol 21: 513-521

  • DOI: https://doi.org/10.1038/nsmb.2822
  • Primary Citation of Related Structures:  
    4P1N, 4P1W

  • PubMed Abstract: 

    Assembly of the preautophagosomal structure (PAS) is essential for autophagy initiation in yeast. Starvation-induced dephosphorylation of Atg13 is required for the formation of the Atg1-Atg13-Atg17-Atg29-Atg31 complex (Atg1 complex), a prerequisite for PAS assembly. However, molecular details underlying these events have not been established. Here we studied the interactions of yeast Atg13 with Atg1 and Atg17 by X-ray crystallography. Atg13 binds tandem microtubule interacting and transport domains in Atg1, using an elongated helix-loop-helix region. Atg13 also binds Atg17, using a short region, thereby bridging Atg1 and Atg17 and leading to Atg1-complex formation. Dephosphorylation of specific serines in Atg13 enhanced its interaction with not only Atg1 but also Atg17. These observations update the autophagy-initiation model as follows: upon starvation, dephosphorylated Atg13 binds both Atg1 and Atg17, and this promotes PAS assembly and autophagy progression.


  • Organizational Affiliation

    1] Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan. [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Atg1 tMIT
A, B
275Kluyveromyces marxianusMutation(s): 0 
Gene Names: ATG1
UniProt
Find proteins for W0T9X4 (Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275))
Explore W0T9X4 
Go to UniProtKB:  W0T9X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0T9X4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Atg13 MIM
C, D
61Kluyveromyces marxianusMutation(s): 0 
UniProt
Find proteins for W0TA43 (Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275))
Explore W0TA43 
Go to UniProtKB:  W0TA43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0TA43
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.995α = 90
b = 96.622β = 93.15
c = 63.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan25111004
Japan Science and TechnologyJapan--
Japan Society for the Promotion of Science (JSPS)Japan2440279
Japan Society for the Promotion of Science (JSPS)Japan24113725

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Data collection
  • Version 1.2: 2014-05-21
    Changes: Database references
  • Version 1.3: 2014-10-01
    Changes: Database references
  • Version 1.4: 2014-12-24
    Changes: Database references
  • Version 2.0: 2020-01-08
    Changes: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Refinement description