3VX8 | pdb_00003vx8

Crystal structure of Arabidopsis thaliana Atg7NTD-Atg3 complex

• PDB DOI: https://doi.org/10.2210/pdb3VX8/pdb

• Classification: LIGASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-11 Released: 2012-11-14 
• Deposition Author(s): Matoba, K., Fujioka, Y., Noda, N.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 
  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

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

• PubMed: 23142983 
• DOI: https://doi.org/10.1038/nsmb.2451
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 138.05 kDa 
• Atom Count: 7,608 
• Modeled Residue Count: 952 
• Deposited Residue Count: 1,230 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like modifier-activating enzyme atg7	A [auth D], B [auth A]	323	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ATG7, APG7, At5g45900, K15I22.10
UniProt
Find proteins for Q94CD5 (Arabidopsis thaliana) Explore Q94CD5  Go to UniProtKB:  Q94CD5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 3	C [auth B], D [auth C]	292	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ATG3, APG3, At5g61500, K11J9.3
UniProt
Find proteins for Q0WWQ1 (Arabidopsis thaliana) Explore Q0WWQ1  Go to UniProtKB:  Q0WWQ1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.52	α = 90
b = 132.683	β = 90
c = 102.805	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Matoba, K., Fujioka, Y., Noda, N.N.

Revision History  

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