6KBN

Crystal structure of Vac8 (del 19-33) bound to Atg13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.

Park, J.Kim, H.I.Jeong, H.Lee, M.Jang, S.H.Yoon, S.Y.Kim, H.Park, Z.Y.Jun, Y.Lee, C.

(2019) Autophagy --: 1-16

  • DOI: 10.1080/15548627.2019.1659615
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can med ...

    Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can mediate diverse functions remains a long-standing question. Vac8 (vacuole related 8) is a multifunctional protein that plays pivotal roles in various autophagic pathways, including piecemeal microautophagy of the nucleus (PMN) and cytoplasm-to-vacuole targeting (Cvt) pathways in the budding yeast Saccharomyces cerevisiae . Vac8 comprises an H1 helix at the N terminus, followed by 12 armadillo repeats. Herein, we report the crystal structure of Vac8 bound to Atg13, a key component of autophagic machinery. The 70-Å extended loop of Atg13 binds to the ARM domain of Vac8 in an antiparallel manner. Structural, biochemical, and in vivo experiments demonstrated that the H1 helix of Vac8 intramolecularly associates with the first ARM and regulates its self-association, which is crucial for Cvt and PMN pathways. The structure of H1 helix-deleted Vac8 complexed with Atg13 reveals that Vac8[Δ19-33]-Atg13 forms a heterotetramer and adopts an extended superhelical structure exclusively employed in the Cvt pathway. Most importantly, comparison of Vac8-Nvj1 and Vac8-Atg13 provides a molecular understanding of how a single ARM domain protein adopts different quaternary structures depending on its associated proteins to differentially regulate 2 closely related but distinct cellular pathways. Abbreviations : Ape1: aminopeptidase I; ARM: armadillo repeat; Atg: autophagy-related; AUC: analytical ultracentrifugation; Cvt: cytoplasm-to-vacuole targeting; DIC: differential interference contrast; GFP: green fluorescent protein; GST: glutathione-S-transferase; ITC: isothermal titration calorimetry; NVJ: nucleus-vacuole junction; PDB: protein data bank; PMN: piecemeal microautophagy of the nucleus; prApe1: precursor Ape1; RMSD: root-mean-square deviation; SAXS: small-angle X-ray scattering; SD-N: nitrogen starvation medium; SEC: size-exclusion chromatography; tAtg13: Atg13 construct comprising residues 567-695; tNvj1: Nvj1 construct comprising residues 229-321; tVac8: Vac8 construct comprising residues 10-515; Vac8: vacuole related 8.


    Organizational Affiliation

    Cell Logistics Research Center, Gwangju Institute of Science and Technology , Gwangju , Republic of Korea.,School of Life Sciences, Gwangju Institute of Science and Technology , Gwangju , Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology , Ulsan , Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein 8
A, C
563Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VAC8 (YEB3)
Find proteins for P39968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39968
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy-related protein 13
B, D
129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATG13 (APG13)
Find proteins for Q06628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ATG13
Go to UniProtKB:  Q06628
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.475α = 90.00
b = 85.268β = 90.00
c = 272.820γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-06-25 
  • Released Date: 2019-11-27 
  • Deposition Author(s): Park, J., Lee, C.

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release