3VX7

Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
E1283Kluyveromyces marxianusMutation(s): 0 
UniProt
Find proteins for L7MTK3 (Kluyveromyces marxianus)
Explore L7MTK3 
Go to UniProtKB:  L7MTK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7MTK3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E2152Kluyveromyces marxianusMutation(s): 0 
UniProt
Find proteins for W0TH64 (Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275))
Explore W0TH64 
Go to UniProtKB:  W0TH64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW0TH64
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.249 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.935α = 90
b = 185.935β = 90
c = 185.935γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

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
  • Version 1.2: 2023-11-08
    Changes: Refinement description