5JM6 | pdb_00005jm6

Structure of Chaetomium thermophilum mApe1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5JM6

This is version 1.4 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 339.19 kDa 
  • Atom Count: 20,685 
  • Modeled Residue Count: 2,670 
  • Deposited Residue Count: 3,114 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aminopeptidase-like protein519Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0065300
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
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
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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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