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
  • Primary Citation of Related Structures:  
    5LXI, 5LXH

  • 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 phosphatidylethanolamine during autophagosome formation ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor-associated protein-like 1B, A [auth D]123Homo sapiensMutation(s): 0 
Gene Names: GABARAPL1GEC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0R8 (Homo sapiens)
Explore Q9H0R8 
Go to UniProtKB:  Q9H0R8
PHAROS:  Q9H0R8
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine protease ATG4BC, D [auth E]10Homo sapiensMutation(s): 0 
Gene Names: ATG4BAPG4BAUTL1KIAA0943
EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4P1 (Homo sapiens)
Explore Q9Y4P1 
Go to UniProtKB:  Q9Y4P1
PHAROS:  Q9Y4P1
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C, D [auth E]L-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  (Full details and data files)

  • 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