Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 179.68 kDa 
• Atom Count: 11408 
• Modelled Residue Count: 1410 
• Deposited Residue Count: 1576 
• Unique protein chains: 2

4GSK

Crystal structure of an Atg7-Atg10 crosslinked complex

• DOI: 10.2210/pdb4GSK/pdb

• Classification: PROTEIN TRANSPORT/LIGASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-08-27 Released: 2012-11-14 
• Deposition Author(s): Kaiser, S.E., Mao, K., Taherbhoy, A.M., Yu, S., Olszewski, J.L., Duda, D.M., Kurinov, I., Deng, A., Fenn, T.D., Klionsky, D.J., Schulman, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.285 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

Literature

Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures.

Kaiser, S.E., Mao, K., Taherbhoy, A.M., Yu, S., Olszewski, J.L., Duda, D.M., Kurinov, I., Deng, A., Fenn, T.D., Klionsky, D.J., Schulman, B.A.

(2012) Nat Struct Mol Biol 19: 1242-1249

• PubMed: 23142976 
• DOI: 10.1038/nsmb.2415
• Primary Citation of Related Structures:  
  4GSJ, 4GSK, 4GSL


• PubMed Abstract: 
  

Core functions of autophagy are mediated by ubiquitin-like protein (UBL) cascades, in which a homodimeric E1 enzyme, Atg7, directs the UBLs Atg8 and Atg12 to their respective E2 enzymes, Atg3 and Atg10. Crystallographic and mutational analyses of yeast (Atg7-Atg3)(2) and (Atg7-Atg10)(2) complexes reveal noncanonical, multisite E1-E2 recognition in autophagy. Atg7's unique N-terminal domain recruits distinctive elements from the Atg3 and Atg10 'backsides'. This, along with E1 and E2 conformational variability, allows presentation of 'frontside' Atg3 and Atg10 active sites to the catalytic cysteine in the C-terminal domain from the opposite Atg7 protomer in the homodimer. Despite different modes of binding, the data suggest that common principles underlie conjugation in both noncanonical and canonical UBL cascades, whereby flexibly tethered E1 domains recruit E2s through surfaces remote from their active sites to juxtapose the E1 and E2 catalytic cysteines.

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Organizational Affiliation: 

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like modifier-activating enzyme ATG7	A, B	615	Saccharomyces cerevisiae S288C	Mutation(s): 3  Gene Names: APG7, ATG7, CVT2, YHR171W
Find proteins for P38862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38862  Go to UniProtKB:  P38862

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like-conjugating enzyme ATG10	C [auth Y], D [auth Z]	173	Saccharomyces cerevisiae S288C	Mutation(s): 2  Gene Names: APG10, ATG10, YLL042C EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for Q07879 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07879  Go to UniProtKB:  Q07879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.285 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.556	α = 90
b = 146.186	β = 90
c = 108.442	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-27 
• Released Date: 2012-11-14 
Deposition Author(s): Kaiser, S.E., Mao, K., Taherbhoy, A.M., Yu, S., Olszewski, J.L., Duda, D.M., Kurinov, I., Deng, A., Fenn, T.D., Klionsky, D.J., Schulman, B.A.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2012-12-19
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description