Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR

Experimental Data Snapshot

  • Resolution: 2.36 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report

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Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR.

Ali, M.G.Wahba, H.M.Igelmann, S.Cyr, N.Ferbeyre, G.Omichinski, J.G.

(2024) Autophagy : 1-20

  • DOI: https://doi.org/10.1080/15548627.2024.2353443
  • Primary Citation of Related Structures:  
    8T31, 8T32, 8T33, 8T35, 8T36, 8T4T

  • PubMed Abstract: 

    The Atg8-family proteins (MAP1LC3/LC3A, LC3B, LC3C, GABARAP, GABARAPL1 and GABARAPL2) play a pivotal role in macroautophagy/autophagy through their ability to help form autophagosomes. Although autophagosomes form in the cytoplasm, nuclear levels of the Atg8-family proteins are significant. Recently, the nuclear/cytoplasmic shuttling of LC3B was shown to require deacetylation of two Lys residues (K49 and K51 in LC3B), which are conserved in Atg8-family proteins. To exit the nucleus, deacetylated LC3B must bind TP53INP2/TP53INP2 (tumor protein p53 inducible nuclear protein 2) through interaction with the LC3-interacting region (LIR) of TP53INP2 (TP53INP2LIR). To examine their selectivity for TP53INP2 and the role of the conserved Lys residues in Atg8-family proteins, we prepared the six human Atg8-family proteins and acetylated variants of LC3A and GABARAP for biophysical and structural characterization of their interactions with the TP53INP2LIR. Isothermal titration calorimetry (ITC) experiments demonstrate that this LIR binds preferentially to GABARAP subfamily proteins, and that only acetylation of the second Lys residue reduces binding to GABARAP and LC3A. Crystal structures of complexes with GABARAP and LC3A (acetylated and deacetylated) define a β-sheet in the TP53INP2LIR that determines the GABARAP selectivity and establishes the importance of acetylation at the second Lys. The in vitro results were confirmed in cells using acetyl-mimetic variants of GABARAP and LC3A to examine nuclear/cytoplasmic shuttling and colocalization with TP53INP2. Together, the results demonstrate that TP53INP2 shows selectivity to the GABARAP subfamily and acetylation at the second Lys of GABARAP and LC3A disrupts key interactions with TP53INP2 required for their nuclear/cytoplasmic shuttling.

  • Organizational Affiliation

    Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A chimera
A, B
134Homo sapiensMutation(s): 0 
Gene Names: TP53INP2C20orf110DORPINHMAP1LC3A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H492 (Homo sapiens)
Explore Q9H492 
Go to UniProtKB:  Q9H492
GTEx:  ENSG00000101460 
Find proteins for Q8IXH6 (Homo sapiens)
Explore Q8IXH6 
Go to UniProtKB:  Q8IXH6
GTEx:  ENSG00000078804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8IXH6Q9H492
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.36 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.004α = 90
b = 47.74β = 95.49
c = 72.902γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references