3X0W

Crystal structure of PLEKHM1 LIR-fused human LC3B_2-119


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.228 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

PLEKHM1 regulates autophagosome-lysosome fusion through HOPS complex and LC3/GABARAP proteins.

McEwan, D.G.Popovic, D.Gubas, A.Terawaki, S.Suzuki, H.Stadel, D.Coxon, F.P.Miranda de Stegmann, D.Bhogaraju, S.Maddi, K.Kirchof, A.Gatti, E.Helfrich, M.H.Wakatsuki, S.Behrends, C.Pierre, P.Dikic, I.

(2015) Mol Cell 57: 39-54

  • DOI: https://doi.org/10.1016/j.molcel.2014.11.006
  • Primary Citation of Related Structures:  
    3X0W

  • PubMed Abstract: 

    The lysosome is the final destination for degradation of endocytic cargo, plasma membrane constituents, and intracellular components sequestered by macroautophagy. Fusion of endosomes and autophagosomes with the lysosome depends on the GTPase Rab7 and the homotypic fusion and protein sorting (HOPS) complex, but adaptor proteins that link endocytic and autophagy pathways with lysosomes are poorly characterized. Herein, we show that Pleckstrin homology domain containing protein family member 1 (PLEKHM1) directly interacts with HOPS complex and contains a LC3-interacting region (LIR) that mediates its binding to autophagosomal membranes. Depletion of PLEKHM1 blocks lysosomal degradation of endocytic (EGFR) cargo and enhances presentation of MHC class I molecules. Moreover, genetic loss of PLEKHM1 impedes autophagy flux upon mTOR inhibition and PLEKHM1 regulates clearance of protein aggregates in an autophagy- and LIR-dependent manner. PLEKHM1 is thus a multivalent endocytic adaptor involved in the lysosome fusion events controlling selective and nonselective autophagy pathways.


  • Organizational Affiliation

    Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, D-60590 Frankfurt (Main), Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3B
A, B
134Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3BMAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ8 (Homo sapiens)
Explore Q9GZQ8 
Go to UniProtKB:  Q9GZQ8
PHAROS:  Q9GZQ8
GTEx:  ENSG00000140941 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZQ8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.228 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.009α = 90
b = 69.009β = 90
c = 119.244γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Refinement description