3RUI

Crystal structure of Atg7C-Atg8 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.906 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8.

Hong, S.B.Kim, B.W.Lee, K.E.Kim, S.W.Jeon, H.Kim, J.Song, H.K.

(2011) Nat.Struct.Mol.Biol. 18: 1323-1330

  • DOI: 10.1038/nsmb.2165
  • Primary Citation of Related Structures:  3RUJ

  • PubMed Abstract: 
  • Autophagy is the degradation of cellular organelles via the lysosomal pathway. The autophagic ubiquitin-like (Ubl) molecule Atg8 is activated by the E1-like enzyme Atg7. As this noncanonical E1 enzyme's domain organization is unique among Ubl-activat ...

    Autophagy is the degradation of cellular organelles via the lysosomal pathway. The autophagic ubiquitin-like (Ubl) molecule Atg8 is activated by the E1-like enzyme Atg7. As this noncanonical E1 enzyme's domain organization is unique among Ubl-activating E1 enzymes, the structural basis for its interactions with Atg8 and partner E2 enzymes remains obscure. Here we present the structure of the N-terminal domain of Atg7, revealing a unique protein fold and interactions with both autophagic E2 enzymes Atg3 and Atg10. The structure of the C-terminal domain of Atg7 in complex with Atg8 shows the mode of dimerization and mechanism of recognition of Atg8. Notably, the catalytic cysteine residue in Atg7 is positioned close to the C-terminal glycine of Atg8, its target for thioester formation, potentially eliminating the need for large conformational rearrangements characteristic of other E1s.


    Organizational Affiliation

    School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like modifier-activating enzyme ATG7
A
340Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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
118Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ATG8 (APG8, AUT7, CVT5)
Find proteins for P38182 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38182
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.906 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.326α = 90.00
b = 71.326β = 90.00
c = 220.916γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references