5JHF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Intrinsically Disordered Protein Atg13 Mediates Supramolecular Assembly of Autophagy Initiation Complexes.

Yamamoto, H.Fujioka, Y.Suzuki, S.W.Noshiro, D.Suzuki, H.Kondo-Kakuta, C.Kimura, Y.Hirano, H.Ando, T.Noda, N.N.Ohsumi, Y.

(2016) Dev.Cell 38: 86-99

  • DOI: 10.1016/j.devcel.2016.06.015

  • PubMed Abstract: 
  • Autophagosome formation in yeast entails starvation-induced assembly of the pre-autophagosomal structure (PAS), in which multiple Atg1 complexes (composed of Atg1, Atg13, and the Atg17-Atg29-Atg31 subcomplex) are initially engaged. However, the molec ...

    Autophagosome formation in yeast entails starvation-induced assembly of the pre-autophagosomal structure (PAS), in which multiple Atg1 complexes (composed of Atg1, Atg13, and the Atg17-Atg29-Atg31 subcomplex) are initially engaged. However, the molecular mechanisms underlying the multimeric assembly of these complexes remain unclear. Using structural and biological techniques, we herein demonstrate that Atg13 has a large intrinsically disordered region (IDR) and interacts with two distinct Atg17 molecules using two binding regions in the IDR. We further reveal that these two binding regions are essential not only for Atg1 complex assembly in vitro, but also for PAS organization in vivo. These findings underscore the structural and functional significance of the IDR of Atg13 in autophagy initiation: Atg13 provides intercomplex linkages between Atg17-Atg29-Atg31 complexes, thereby leading to supramolecular self-assembly of Atg1 complexes, in turn accelerating the initial events of autophagy, including autophosphorylation of Atg1, recruitment of Atg9 vesicles, and phosphorylation of Atg9 by Atg1.


    Organizational Affiliation

    Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, Japan.,Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan. Electronic address: yohsumi@iri.titech.ac.jp.,Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan.,Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.,Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan.,Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan. Electronic address: nn@bikaken.or.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KLTH0D11660p
A, D
87Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)Mutation(s): 0 
Find proteins for C5DF24 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DF24
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
KLTH0C07942p
B, E
151Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)Mutation(s): 0 
Find proteins for C5DEB9 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DEB9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
KLTH0D15642p
C, F
413Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)Mutation(s): 0 
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, H
13Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)Mutation(s): 0 
Find proteins for C5DB94 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DB94
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Atg13 17LR
I, J
13Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284)Mutation(s): 0 
Find proteins for C5DB94 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Go to UniProtKB:  C5DB94
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 147.956α = 90.00
b = 64.043β = 109.91
c = 184.387γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release