4P1W

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 2.0 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:  
    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 ...

    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] Core Research for Evolutionary Science and Technology (CREST), Japan Science and Technology Agency, Tokyo, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Atg29A, D74Lachancea 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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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Atg31B, E151Lachancea 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Atg17C, F413Lachancea 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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UniProt GroupC5DFJ6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Atg13 17BRG13Lachancea thermotolerans CBS 6340Mutation(s): 0 
Gene Names: KLTH0A00704g
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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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.348α = 90
b = 63.989β = 109.25
c = 184.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

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

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 2.0: 2020-01-08
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary