5JH9

Crystal structure of prApe1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates

Yamasaki, A.Watanabe, Y.Adachi, W.Suzuki, K.Matoba, K.Kirisako, H.Kumeta, H.Nakatogawa, H.Ohsumi, Y.Inagaki, F.Noda, N.N.

(2016) Cell Rep 16: 19-27

  • DOI: 10.1016/j.celrep.2016.05.066
  • Primary Citation of Related Structures:  
    5JGE, 5JGF, 5JHC, 5JH9

  • PubMed Abstract: 
  • Selective autophagy mediates the degradation of various cargoes, including protein aggregates and organelles, thereby contributing to cellular homeostasis. Cargo receptors ensure selectivity by tethering specific cargo to lipidated Atg8 at the isolation membrane ...

    Selective autophagy mediates the degradation of various cargoes, including protein aggregates and organelles, thereby contributing to cellular homeostasis. Cargo receptors ensure selectivity by tethering specific cargo to lipidated Atg8 at the isolation membrane. However, little is known about the structural requirements underlying receptor-mediated cargo recognition. Here, we report structural, biochemical, and cell biological analysis of the major selective cargo protein in budding yeast, aminopeptidase I (Ape1), and its complex with the receptor Atg19. The Ape1 propeptide has a trimeric coiled-coil structure, which tethers dodecameric Ape1 bodies together to form large aggregates. Atg19 disassembles the propeptide trimer and forms a 2:1 heterotrimer, which not only blankets the Ape1 aggregates but also regulates their size. These receptor activities may promote elongation of the isolation membrane along the aggregate surface, enabling sequestration of the cargo with high specificity.


    Organizational Affiliation

    Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan. Electronic address: nn@bikaken.or.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar aminopeptidase 1A, B, C, D516Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: APE1APILAP4YSC1YKL103CYKL455
EC: 3.4.11.22
UniProt
Find proteins for P14904 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14904 
Go to UniProtKB:  P14904
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.428α = 90
b = 140.428β = 90
c = 348.922γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations