4WAA | pdb_00004waa

Crystal structure of Nix LIR-fused human LC3B_2-119

• PDB DOI: https://doi.org/10.2210/pdb4WAA/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-29 Released: 2015-09-09 
• Deposition Author(s): Suzuki, H., Ravichandran, A.C., Dobson, R.C.J., Novak, I., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.273 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

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

• PubMed: 28442745 
• DOI: https://doi.org/10.1038/s41598-017-01258-6
• Primary Citation Related Structures: 
  4WAA


• 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 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.

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Organizational Affiliation: 
• Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438, Frankfurt, Germany.
Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, 8020, New Zealand.
Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan.
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.
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.
W. Harry Feinstone Department of Molecular Microbiology & Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, D-60438, Frankfurt, Germany. [e-mail].
Institute of Biochemistry II, Goethe University Medical School and Buchmann Institute for Molecular Life Sciences, D-60590, Frankfurt, Germany.
Systems Biology of Cell Death Mechanisms, German Cancer Research Center (DKFZ), Heidelberg University Hospital; Bioquant, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.
Department of Surgery, Heidelberg University Hospital; Bioquant, Im Neuenheimer Feld 267, D-69120, Heidelberg, Germany.
School of Medicine, University of Split, Šoltanska 2, HR-21000, Split, Croatia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.17 kDa 
• Atom Count: 2,194 
• Modeled Residue Count: 251 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated proteins 1A/1B light chain 3B	A, B	134	Homo sapiens	Mutation(s): 0  Gene Names: MAP1LC3B, MAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ8 (Homo sapiens) Explore Q9GZQ8  Go to UniProtKB:  Q9GZQ8
PHAROS:  Q9GZQ8 GTEx:  ENSG00000140941

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.273 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.385	α = 90
b = 67.385	β = 90
c = 116.875	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Suzuki, H., Ravichandran, A.C., Dobson, R.C.J., Novak, I., Wakatsuki, S.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description