3VX8

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.

Yamaguchi, M.Matoba, K.Sawada, R.Fujioka, Y.Nakatogawa, H.Yamamoto, H.Kobashigawa, Y.Hoshida, H.Akada, R.Ohsumi, Y.Noda, N.N.Inagaki, F.

(2012) Nat Struct Mol Biol 19: 1250-1256

  • DOI: https://doi.org/10.1038/nsmb.2451
  • Primary Citation of Related Structures:  
    3VX6, 3VX7, 3VX8

  • PubMed Abstract: 

    Autophagy requires ubiquitin-like Atg8 and Atg12 conjugation systems, where Atg7 has a critical role as the sole E1 enzyme. Although Atg7 recognizes two distinct E2s, Atg3 and Atg10, it is not understood how Atg7 correctly loads these E2s with their cognate ubiquitin-like proteins, Atg8 and Atg12. Here, we report the crystal structures of the N-terminal domain of Atg7 bound to Atg10 or Atg3 of thermotolerant yeast and plant homologs. The observed Atg7-Atg10 and Atg7-Atg3 interactions, which resemble each other but are quite distinct from the canonical E1-E2 interaction, makes Atg7 suitable for transferring Atg12 to Atg10 and Atg8 to Atg3 by a trans mechanism. Notably, in vitro experiments showed that Atg7 loads Atg3 and Atg10 with Atg8 and Atg12 in a nonspecific manner, which suggests that cognate conjugate formation in vivo is not an intrinsic quality of Atg7.


  • Organizational Affiliation

    Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like modifier-activating enzyme atg7A [auth D],
B [auth A]
323Arabidopsis thalianaMutation(s): 0 
Gene Names: ATG7APG7At5g45900K15I22.10
UniProt
Find proteins for Q94CD5 (Arabidopsis thaliana)
Explore Q94CD5 
Go to UniProtKB:  Q94CD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94CD5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Autophagy-related protein 3C [auth B],
D [auth C]
292Arabidopsis thalianaMutation(s): 0 
Gene Names: ATG3APG3At5g61500K11J9.3
UniProt
Find proteins for Q0WWQ1 (Arabidopsis thaliana)
Explore Q0WWQ1 
Go to UniProtKB:  Q0WWQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0WWQ1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.52α = 90
b = 132.683β = 90
c = 102.805γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references