4P1W

Crystal structure of Atg13(17BR)-Atg17-Atg29-Atg31 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
Atg29
A, D
74Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)
Find proteins for C5DF24 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DF24
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Atg31
B, E
151Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)
Find proteins for C5DEB9 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DEB9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Atg17
C, F
413Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)
Find proteins for C5DFJ6 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DFJ6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Atg13 17BR
G
13Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)
Find proteins for C5DB94 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DB94
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.257 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 148.348α = 90.00
b = 63.989β = 109.25
c = 184.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

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