5DPT

Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and functional analysis of the GABARAP interaction motif (GIM).

Rogov, V.V.Stolz, A.Ravichandran, A.C.Rios-Szwed, D.O.Suzuki, H.Kniss, A.Lohr, F.Wakatsuki, S.Dotsch, V.Dikic, I.Dobson, R.C.McEwan, D.G.

(2017) EMBO Rep. 18: 1382-1396

  • DOI: 10.15252/embr.201643587
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Through the canonical LC3 interaction motif (LIR), [W/F/Y]-X <sub>1 </sub>-X <sub>2 </sub>-[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors s ...

    Through the canonical LC3 interaction motif (LIR), [W/F/Y]-X 1 -X 2 -[I/L/V], protein complexes are recruited to autophagosomes to perform their functions as either autophagy adaptors or receptors. How these adaptors/receptors selectively interact with either LC3 or GABARAP families remains unclear. Herein, we determine the range of selectivity of 30 known core LIR motifs towards individual LC3s and GABARAPs. From these, we define a G ABARAP I nteraction M otif (GIM) sequence ([W/F]-[V/I]-X 2 -V) that the adaptor protein PLEKHM1 tightly conforms to. Using biophysical and structural approaches, we show that the PLEKHM1-LIR is indeed 11-fold more specific for GABARAP than LC3B. Selective mutation of the X 1 and X 2 positions either completely abolished the interaction with all LC3 and GABARAPs or increased PLEKHM1-GIM selectivity 20-fold towards LC3B. Finally, we show that conversion of p62/SQSTM1, FUNDC1 and FIP200 LIRs into our newly defined GIM, by introducing two valine residues, enhances their interaction with endogenous GABARAP over LC3B. The identification of a GABARAP-specific interaction motif will aid the identification and characterization of the expanding array of autophagy receptor and adaptor proteins and their in vivo functions.


    Organizational Affiliation

    Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand ivan.dikic@biochem2.de renwick.dobson@canterbury.ac.nz d.g.mcewan@dundee.ac.uk.,Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany.,Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany.,Structural Biology Research Centre, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba Ibaraki, Japan.,Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.,Structural Biology (School of Medicine), Beckman Center B105, Stanford, CA, USA.,Institute of Biochemistry II, Goethe University School of Medicine, Frankfurt (Main), Germany ivan.dikic@biochem2.de renwick.dobson@canterbury.ac.nz d.g.mcewan@dundee.ac.uk.,Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Vic., Australia.,Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.,Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,Gamma-aminobutyric acid receptor-associated protein-like 1
A, B
132Homo sapiensMutation(s): 0 
Gene Names: GABARAPL1 (GEC1), PLEKHM1 (KIAA0356)
Find proteins for Q9H0R8 (Homo sapiens)
Go to Gene View: GABARAPL1
Go to UniProtKB:  Q9H0R8
Find proteins for Q9Y4G2 (Homo sapiens)
Go to Gene View: PLEKHM1
Go to UniProtKB:  Q9Y4G2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.791α = 90.00
b = 84.791β = 90.00
c = 105.440γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references, Derived calculations