5YEC

Crystal structure of Atg7CTD-Atg8-MgATP complex in form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.147 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.

Yamaguchi, M.Satoo, K.Suzuki, H.Fujioka, Y.Ohsumi, Y.Inagaki, F.Noda, N.N.

(2018) J. Mol. Biol. 430: 249-257

  • DOI: 10.1016/j.jmb.2017.12.002

  • PubMed Abstract: 
  • Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal ...

    Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal Gly116 of Atg8 using ATP. Here, we report the crystal structure of Atg8 bound to the C-terminal domain of Atg7 in an unprecedented mode. Atg8 neither contacts with the central β-sheet nor binds to the catalytic site of Atg7, both of which were observed in previously reported Atg7-Atg8 structures. Instead, Atg8 binds to the C-terminal α-helix and crossover loop, thereby changing the autoinhibited conformation of the crossover loop observed in the free Atg7 structure into a short helix and a disordered loop. Mutational analyses suggested that this interaction mode is important for the activation reaction. We propose that Atg7 recognizes Atg8 through multiple steps, which would be necessary to induce a conformational change in Atg7 that is optimal for the activation reaction.


    Organizational Affiliation

    Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan.,Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan.,Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan.,Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan. Electronic address: nn@bikaken.or.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like modifier-activating enzyme ATG7
A, C
340Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATG7 (APG7, CVT2)
Find proteins for P38862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ATG7
Go to UniProtKB:  P38862
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy-related protein 8
B, D
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: ATG8 (APG8, AUT7, CVT5)
Find proteins for P38182 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38182
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.147 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 138.995α = 90.00
b = 138.995β = 90.00
c = 134.368γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release