5DPW

Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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:  
    5DPR, 5DPS, 5DPT, 5DPW

  • PubMed Abstract: 
  • 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 ...

    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

    Division of Cell Signalling & Immunology, School of Life Sciences, University of Dundee, Dundee, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3CA, C, E, G, I, K, M, O118Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3C
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXW4 (Homo sapiens)
Explore Q9BXW4 
Go to UniProtKB:  Q9BXW4
PHAROS:  Q9BXW4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pleckstrin homology domain-containing family M member 1B, D, F, H, J, L, N, P14Homo sapiensMutation(s): 0 
Gene Names: PLEKHM1KIAA0356
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4G2 (Homo sapiens)
Explore Q9Y4G2 
Go to UniProtKB:  Q9Y4G2
PHAROS:  Q9Y4G2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.14α = 89.96
b = 73.225β = 89.99
c = 89.048γ = 77.31
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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