4HPQ

Crystal Structure of the Atg17-Atg31-Atg29 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Architecture of the atg17 complex as a scaffold for autophagosome biogenesis.

Ragusa, M.J.Stanley, R.E.Hurley, J.H.

(2012) Cell 151: 1501-1512

  • DOI: https://doi.org/10.1016/j.cell.2012.11.028
  • Primary Citation of Related Structures:  
    4HPQ

  • PubMed Abstract: 

    Macroautophagy is a bulk clearance mechanism in which the double-membraned phagophore grows and engulfs cytosolic material. In yeast, the phagophore nucleates from a cluster of 20-30 nm diameter Atg9-containing vesicles located at a multiprotein assembly known as the preautophagosomal structure (PAS). The crystal structure of a 2:2:2 complex of the earliest acting PAS proteins, Atg17, Atg29, and Atg31, was solved at 3.05 Å resolution. Atg17 is crescent shaped with a 10 nm radius of curvature. Dimerization of the Atg17-Atg31-Atg29 complex is critical for both PAS formation and autophagy, and each dimer contains two separate and complete crescents. Upon induction of autophagy, Atg17-Atg31-Atg29 assembles with Atg1 and Atg13, which in turn initiates the formation of the phagophore. The C-terminal EAT domain of Atg1 was shown to sense membrane curvature, dimerize, and tether lipid vesicles. These data suggest a structural mechanism for the organization of Atg9 vesicles into the early phagophore.


  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Atg29
A, D
69Lachancea thermotolerans CBS 6340Mutation(s): 0 
UniProt
Find proteins for C5DF24 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Explore C5DF24 
Go to UniProtKB:  C5DF24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5DF24
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Atg31
B, E
159Lachancea thermotolerans CBS 6340Mutation(s): 2 
UniProt
Find proteins for C5DEB9 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Explore C5DEB9 
Go to UniProtKB:  C5DEB9
Entity Groups  
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UniProt GroupC5DEB9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Atg17
C, F
413Lachancea thermotolerans CBS 6340Mutation(s): 0 
UniProt
Find proteins for C5DFJ6 (Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284))
Explore C5DFJ6 
Go to UniProtKB:  C5DFJ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC5DFJ6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.37α = 90
b = 64.2β = 110.79
c = 184.21γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2018-01-10
    Changes: Source and taxonomy, Structure summary
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references