Crystal structure of Optineurin LIR-fused human LC3B_2-119

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural basis for phosphorylation-triggered autophagic clearance of Salmonella

Rogov, V.V.Suzuki, H.Fiskin, E.Wild, P.Kniss, A.Rozenknop, A.Kato, R.Kawasaki, M.McEwan, D.G.Lohr, F.Guntert, P.Dikic, I.Wakatsuki, S.Dotsch, V.

(2013) Biochem J 454: 459-466

  • DOI: https://doi.org/10.1042/BJ20121907
  • Primary Citation of Related Structures:  
    2LUE, 3VTU, 3VTV, 3VTW

  • PubMed Abstract: 

    Selective autophagy is mediated by the interaction of autophagy modifiers and autophagy receptors that also bind to ubiquitinated cargo. Optineurin is an autophagy receptor that plays a role in the clearance of cytosolic Salmonella. The interaction between receptors and modifiers is often relatively weak, with typical values for the dissociation constant in the low micromolar range. The interaction of optineurin with autophagy modifiers is even weaker, but can be significantly enhanced through phosphorylation by the TBK1 {TANK [TRAF (tumour-necrosis-factor-receptor-associated factor)-associated nuclear factor κB activator]-binding kinase 1}. In the present study we describe the NMR and crystal structures of the autophagy modifier LC3B (microtubule-associated protein light chain 3 beta) in complex with the LC3 interaction region of optineurin either phosphorylated or bearing phospho-mimicking mutations. The structures show that the negative charge induced by phosphorylation is recognized by the side chains of Arg¹¹ and Lys⁵¹ in LC3B. Further mutational analysis suggests that the replacement of the canonical tryptophan residue side chain of autophagy receptors with the smaller phenylalanine side chain in optineurin significantly weakens its interaction with the autophagy modifier LC3B. Through phosphorylation of serine residues directly N-terminally located to the phenylalanine residue, the affinity is increased to the level normally seen for receptor-modifier interactions. Phosphorylation, therefore, acts as a switch for optineurin-based selective autophagy.

  • Organizational Affiliation

    Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-van-Laue Str. 9, 60438 Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Optineurin, microtubule-associated proteins 1A/1B light chain 3B134Homo sapiensMutation(s): 5 
Gene Names: MAP1LC3BMAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CV9 (Homo sapiens)
Explore Q96CV9 
Go to UniProtKB:  Q96CV9
GTEx:  ENSG00000123240 
Find proteins for Q9GZQ8 (Homo sapiens)
Explore Q9GZQ8 
Go to UniProtKB:  Q9GZQ8
GTEx:  ENSG00000140941 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ96CV9Q9GZQ8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.2α = 90
b = 53β = 90
c = 60.96γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description