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 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.devcel.2016.06.015
  • Primary Citation of Related Structures:  
    5JHF

  • 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 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

    Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KLTH0D11660p
A, D
87Lachancea thermotolerans CBS 6340Mutation(s): 0 
Gene Names: KLTH0D11660g
UniProt
Find proteins for C5DF24 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
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UniProt GroupC5DF24
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
KLTH0C07942p
B, E
151Lachancea thermotolerans CBS 6340Mutation(s): 0 
Gene Names: KLTH0C07942g
UniProt
Find proteins for C5DEB9 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
KLTH0D15642p
C, F
413Lachancea thermotolerans CBS 6340Mutation(s): 0 
Gene Names: KLTH0D15642g
UniProt
Find proteins for C5DFJ6 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Atg13 17BR
G, H
13Lachancea thermotoleransMutation(s): 0 
UniProt
Find proteins for C5DB94 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Atg13 17LR
I, J
13Lachancea thermotoleransMutation(s): 0 
UniProt
Find proteins for C5DB94 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Explore C5DB94 
Go to UniProtKB:  C5DB94
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UniProt GroupC5DB94
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.956α = 90
b = 64.043β = 109.91
c = 184.387γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary