4WAA

Crystal structure of Nix LIR-fused human LC3B_2-119


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Phosphorylation of the mitochondrial autophagy receptor Nix enhances its interaction with LC3 proteins.

Rogov, V.V.Suzuki, H.Marinkovic, M.Lang, V.Kato, R.Kawasaki, M.Buljubasic, M.Sprung, M.Rogova, N.Wakatsuki, S.Hamacher-Brady, A.Dotsch, V.Dikic, I.Brady, N.R.Novak, I.

(2017) Sci Rep 7: 1131-1131

  • DOI: 10.1038/s41598-017-01258-6

  • PubMed Abstract: 
  • The mitophagy receptor Nix interacts with LC3/GABARAP proteins, targeting mitochondria into autophagosomes for degradation. Here we present evidence for phosphorylation-driven regulation of the Nix:LC3B interaction. Isothermal titration calorimetry a ...

    The mitophagy receptor Nix interacts with LC3/GABARAP proteins, targeting mitochondria into autophagosomes for degradation. Here we present evidence for phosphorylation-driven regulation of the Nix:LC3B interaction. Isothermal titration calorimetry and NMR indicate a ~100 fold enhanced affinity of the serine 34/35-phosphorylated Nix LC3-interacting region (LIR) to LC3B and formation of a very rigid complex compared to the non-phosphorylated sequence. Moreover, the crystal structure of LC3B in complex with the Nix LIR peptide containing glutamic acids as phosphomimetic residues and NMR experiments revealed that LIR phosphorylation stabilizes the Nix:LC3B complex via formation of two additional hydrogen bonds between phosphorylated serines of Nix LIR and Arg11, Lys49 and Lys51 in LC3B. Substitution of Lys51 to Ala in LC3B abrogates binding of a phosphomimetic Nix mutant. Functionally, serine 34/35 phosphorylation enhances autophagosome recruitment to mitochondria in HeLa cells. Together, this study provides cellular, biochemical and biophysical evidence that phosphorylation of the LIR domain of Nix enhances mitophagy receptor engagement.


    Organizational Affiliation

    School of Medicine, University of Split, Šoltanska 2, HR-21000, Split, Croatia. ivana.novak@mefst.hr.,Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438, Frankfurt, Germany.,Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan.,Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438, Frankfurt, Germany. vdoetsch@em.uni-frankfurt.de.,Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8020, New Zealand.,Systems Biology of Cell Death Mechanisms, German Cancer Research Center (DKFZ), Heidelberg University Hospital; Bioquant, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,School of Medicine, University of Split, Šoltanska 2, HR-21000, Split, Croatia.,Lysosomal Systems Biology, German Cancer Research Center (DKFZ), Bioquant, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,Department of Surgery, Heidelberg University Hospital; Bioquant, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.,W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.,Faculty of Science, University of Split, Ruđera Boškovića 33, HR-21000, Split, Croatia.,Structural Biology (School of Medicine), Beckman Center B105, 279 Campus Drive, Stanford, CA, 94305-5126, USA.,Institute of Biochemistry II, Goethe University Medical School and Buchmann Institute for Molecular Life Sciences, D-60590, Frankfurt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3B
A, B
134Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3B (MAP1ALC3)
Find proteins for Q9GZQ8 (Homo sapiens)
Go to Gene View: MAP1LC3B
Go to UniProtKB:  Q9GZQ8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 67.385α = 90.00
b = 67.385β = 90.00
c = 116.875γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references