Crystal structure of yeast aminopeptidase 1 (Ape1)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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This is version 1.3 of the entry. See complete history


Structure of yeast Ape1 and its role in autophagic vesicle formation.

Su, M.Y.Peng, W.H.Ho, M.R.Su, S.C.Chang, Y.C.Chen, G.C.Chang, C.I.

(2015) Autophagy 11: 1580-1593

  • DOI: https://doi.org/10.1080/15548627.2015.1067363
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In Saccharomyces cerevisiae, a constitutive biosynthetic transport pathway, termed the cytoplasm-to-vacuole targeting (Cvt) pathway, sequesters precursor aminopeptidase I (prApe1) dodecamers in the form of a large complex into a Cvt vesicle using autophagic machinery, targeting it into the vacuole (the yeast lysosome) where it is proteolytically processed into its mature form, Ape1, by removal of an amino-terminal 45-amino acid propeptide. prApe1 is thought to serve as a scaffolding cargo critical for the assembly of the Cvt vesicle by presenting the propeptide to mediate higher-ordered complex formation and autophagic receptor recognition. Here we report the X-ray crystal structure of Ape1 at 2.5 Å resolution and reveal its dodecameric architecture consisting of dimeric and trimeric units, which associate to form a large tetrahedron. The propeptide of prApe1 exhibits concentration-dependent oligomerization and forms a stable tetramer. Structure-based mutagenesis demonstrates that disruption of the inter-subunit interface prevents dodecameric assembly and vacuolar targeting in vivo despite the presence of the propeptide. Furthermore, by examining the vacuolar import of propeptide-fused exogenous protein assemblies with different quaternary structures, we found that 3-dimensional spatial distribution of propeptides presented by a scaffolding cargo is essential for the assembly of the Cvt vesicle for vacuolar delivery. This study describes a molecular framework for understanding the mechanism of Cvt or autophagosomal biogenesis in selective macroautophagy.

  • Organizational Affiliation

    a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar aminopeptidase 1
A, B, C, D
470Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for P14904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14904 
Go to UniProtKB:  P14904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14904
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: H 3
  • Diffraction Data: https://doi.org/10.15785/SBGRID/87
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.171α = 90
b = 140.171β = 90
c = 348.677γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
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: 2015-08-12
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description