5LXI

GABARAP-L1 ATG4B LIR Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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: 2
MoleculeChainsSequence LengthOrganismDetails
Cysteine protease ATG4BC, E10Homo sapiensMutation(s): 0 
Gene Names: ATG4BAPG4BAUTL1KIAA0943
EC: 3.4.22
Find proteins for Q9Y4P1 (Homo sapiens)
Explore Q9Y4P1 
Go to UniProtKB:  Q9Y4P1
NIH Common Fund Data Resources
PHAROS  Q9Y4P1
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid receptor-associated protein-like 1B, D123Homo sapiensMutation(s): 0 
Gene Names: GABARAPL1GEC1
Find proteins for Q9H0R8 (Homo sapiens)
Explore Q9H0R8 
Go to UniProtKB:  Q9H0R8
NIH Common Fund Data Resources
PHAROS  Q9H0R8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download CCD File 
D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

Download CCD File 
D
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C,EL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.888α = 90
b = 72.377β = 99.21
c = 30.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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