5LXH

GABARAP-L1 ATG4B LIR Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8.

Skytte Rasmussen, M.Mouilleron, S.Kumar Shrestha, B.Wirth, M.Lee, R.Bowitz Larsen, K.Abudu Princely, Y.O'Reilly, N.Sjttem, E.Tooze, S.A.Lamark, T.Johansen, T.

(2017) Autophagy 13: 834-853

  • DOI: 10.1080/15548627.2017.1287651
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cysteine protease ATG4B cleaves off one or more C-terminal residues of the inactive proform of proteins of the ortholog and paralog LC3 and GABARAP subfamilies of yeast Atg8 to expose a C-terminal glycine that is conjugated to phosphatidylethanol ...

    The cysteine protease ATG4B cleaves off one or more C-terminal residues of the inactive proform of proteins of the ortholog and paralog LC3 and GABARAP subfamilies of yeast Atg8 to expose a C-terminal glycine that is conjugated to phosphatidylethanolamine during autophagosome formation. We show that ATG4B contains a C-terminal LC3-interacting region (LIR) motif important for efficient binding to and cleavage of LC3 and GABARAP proteins. We solved the crystal structures of the GABARAPL1-ATG4B C-terminal LIR complex. Analyses of the structures and in vitro binding assays, using specific point mutants, clearly showed that the ATG4B LIR binds via electrostatic-, aromatic HP1 and hydrophobic HP2 pocket interactions. Both these interactions and the catalytic site-substrate interaction contribute to binding between LC3s or GABARAPs and ATG4B. We also reveal an unexpected role for ATG4B in stabilizing the unlipidated forms of GABARAP and GABARAPL1. In mouse embryonic fibroblast (MEF) atg4b knockout cells, GABARAP and GABARAPL1 were unstable and degraded by the proteasome. Strikingly, the LIR motif of ATG4B was required for stabilization of the unlipidated forms of GABARAP and GABARAPL1 in cells.


    Organizational Affiliation

    a Molecular Cancer Research Group, Department of Medical Biology , University of Tromsø -The Arctic University of Norway , Tromsø , Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid receptor-associated protein-like 1
A, B, C
123Homo sapiensMutation(s): 0 
Gene Names: GABARAPL1 (GEC1)
Find proteins for Q9H0R8 (Homo sapiens)
Go to Gene View: GABARAPL1
Go to UniProtKB:  Q9H0R8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cysteine protease ATG4B
E, F, G
10Homo sapiensMutation(s): 0 
Gene Names: ATG4B (APG4B, AUTL1, KIAA0943)
EC: 3.4.22.-
Find proteins for Q9Y4P1 (Homo sapiens)
Go to Gene View: ATG4B
Go to UniProtKB:  Q9Y4P1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.520α = 90.00
b = 79.885β = 90.00
c = 97.643γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-02-15
    Type: Database references
  • Version 1.2: 2017-03-22
    Type: Database references
  • Version 1.3: 2017-05-31
    Type: Database references