4P1N

Crystal structure of Atg1-Atg13 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1038/nsmb.2822
  • Primary Citation of Related Structures:  

  • 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 f ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Atg1 tMIT
A, B
275Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275)Mutation(s): 0 
Gene Names: ATG1
EC: 2.7.11.1
Find proteins for W0T9X4 (Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275))
Go to UniProtKB:  W0T9X4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Atg13 MIM
C, D
61Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275)Mutation(s): 0 
Gene Names: ATG13
Find proteins for W0TA43 (Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275))
Go to Gene View: ATG13
Go to UniProtKB:  W0TA43
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.995α = 90.00
b = 96.622β = 93.15
c = 63.330γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25111004
Japan Science and Technology AgencyJapan--
Japan Society for the Promotion of ScienceJapan2440279
Japan Society for the Promotion of ScienceJapan24113725

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-14
    Type: Data collection
  • Version 1.2: 2014-05-21
    Type: Database references
  • Version 1.3: 2014-10-01
    Type: Database references
  • Version 1.4: 2014-12-24
    Type: Database references