4GDL

Crystal Structure of Human Atg12~Atg5 Conjugate in Complex with an N-terminal Fragment of Atg16L1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.875 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy.

Otomo, C.Metlagel, Z.Takaesu, G.Otomo, T.

(2013) Nat.Struct.Mol.Biol. 20: 59-66

  • DOI: 10.1038/nsmb.2431
  • Primary Citation of Related Structures:  4GDK

  • PubMed Abstract: 
  • The autophagy factor ATG12~ATG5 conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 family. The crystal structure of the human ATG12~ATG5 conjugate bound to the N-terminal region of ATG16L1, the factor th ...

    The autophagy factor ATG12~ATG5 conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 family. The crystal structure of the human ATG12~ATG5 conjugate bound to the N-terminal region of ATG16L1, the factor that recruits the conjugate to autophagosomal membranes, reveals an integrated architecture in which ATG12 docks onto ATG5 through conserved residues. ATG12 and ATG5 are oriented such that other conserved residues on each molecule, including the conjugation junction, form a continuous surface patch. Mutagenesis data support the importance of both the interface between ATG12 and ATG5 and the continuous patch for E3 activity. The ATG12~ATG5 conjugate interacts with the E2 enzyme ATG3 with high affinity through another surface location that is exclusive to ATG12, suggesting a different role of the continuous patch in E3 activity. These findings provide a foundation for understanding the mechanism of LC3 lipidation.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein ATG12
A
91Homo sapiensGene Names: ATG12 (APG12, APG12L)
Find proteins for O94817 (Homo sapiens)
Go to Gene View: ATG12
Go to UniProtKB:  O94817
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy protein 5
B
275Homo sapiensGene Names: ATG5 (APG5L, ASP)
Find proteins for Q9H1Y0 (Homo sapiens)
Go to Gene View: ATG5
Go to UniProtKB:  Q9H1Y0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Autophagy-related protein 16-1
C
36Homo sapiensGene Names: ATG16L1 (APG16L)
Find proteins for Q676U5 (Homo sapiens)
Go to Gene View: ATG16L1
Go to UniProtKB:  Q676U5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.875 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.601α = 90.00
b = 58.399β = 130.04
c = 91.802γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2013-01-16
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description