Structure of Chaetomium thermophilum mApe1

Experimental Data Snapshot

  • Resolution: 2.76 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle.

Bertipaglia, C.Schneider, S.Jakobi, A.J.Tarafder, A.K.Bykov, Y.S.Picco, A.Kukulski, W.Kosinski, J.Hagen, W.J.Ravichandran, A.C.Wilmanns, M.Kaksonen, M.Briggs, J.A.Sachse, C.

(2016) EMBO Rep 17: 1044-1060

  • DOI: https://doi.org/10.15252/embr.201541960
  • Primary Citation of Related Structures:  
    5JM0, 5JM6, 5JM9

  • PubMed Abstract: 

    Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles remain to be elucidated. We utilize the yeast cytoplasm-to-vacuole targeting (Cvt) pathway, a prototype of selective autophagy, together with a multi-scale analysis approach to study the molecular structure of Cvt vesicles. We report the oligomeric nature of the major Cvt cargo Ape1 with a combined 2.8 Å X-ray and negative stain EM structure, as well as the secondary cargo Ams1 with a 6.3 Å cryo-EM structure. We show that the major dodecameric cargo prApe1 exhibits a tendency to form higher-order chain structures that are broken upon interaction with the receptor Atg19 in vitro The stoichiometry of these cargo-receptor complexes is key to maintaining the size of the Cvt aggregate in vivo Using correlative light and electron microscopy, we further visualize key stages of Cvt vesicle biogenesis. Our findings suggest that Atg19 interaction limits Ape1 aggregate size while serving as a vehicle for vacuolar delivery of tetrameric Ams1.

  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminopeptidase-like protein519Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0065300
Find proteins for G0SG74 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SG74 
Go to UniProtKB:  G0SG74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SG74
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth E]
J [auth E]
K [auth F]
G [auth A],
H [auth A],
I [auth E],
J [auth E],
K [auth F],
L [auth F],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.76 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.019α = 90
b = 143.894β = 90
c = 201.315γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-07-13
    Changes: Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description