Structure of Partial Beta-Hairpin LIR from FNIP2 Bound to GABARAP

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report

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GABARAP sequesters the FLCN-FNIP tumor suppressor complex to couple autophagy with lysosomal biogenesis.

Goodwin, J.M.Walkup 4th, W.G.Hooper, K.Li, T.Kishi-Itakura, C.Ng, A.Lehmberg, T.Jha, A.Kommineni, S.Fletcher, K.Garcia-Fortanet, J.Fan, Y.Tang, Q.Wei, M.Agrawal, A.Budhe, S.R.Rouduri, S.R.Baird, D.Saunders, J.Kiselar, J.Chance, M.R.Ballabio, A.Appleton, B.A.Brumell, J.H.Florey, O.Murphy, L.O.

(2021) Sci Adv 7: eabj2485-eabj2485

  • DOI: https://doi.org/10.1126/sciadv.abj2485
  • Primary Citation of Related Structures:  
    7LSW, 7LT6

  • PubMed Abstract: 

    Adaptive changes in lysosomal capacity are driven by the transcription factors TFEB and TFE3 in response to increased autophagic flux and endolysosomal stress, yet the molecular details of their activation are unclear. LC3 and GABARAP members of the ATG8 protein family are required for selective autophagy and sensing perturbation within the endolysosomal system. Here, we show that during the conjugation of ATG8 to single membranes (CASM), Parkin-dependent mitophagy, and Salmonella -induced xenophagy, the membrane conjugation of GABARAP, but not LC3, is required for activation of TFEB/TFE3 to control lysosomal capacity. GABARAP directly binds to a previously unidentified LC3-interacting motif (LIR) in the FLCN/FNIP tumor suppressor complex and mediates sequestration to GABARAP-conjugated membrane compartments. This disrupts FLCN/FNIP GAP function toward RagC/D, resulting in impaired substrate-specific mTOR-dependent phosphorylation of TFEB. Thus, the GABARAP-FLCN/FNIP-TFEB axis serves as a molecular sensor that coordinates lysosomal homeostasis with perturbations and cargo flux within the autophagy-lysosomal network.

  • Organizational Affiliation

    Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
A, B, C
139Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P278 (Homo sapiens)
Explore Q9P278 
Go to UniProtKB:  Q9P278
GTEx:  ENSG00000052795 
Find proteins for O95166 (Homo sapiens)
Explore O95166 
Go to UniProtKB:  O95166
PHAROS:  O95166
GTEx:  ENSG00000170296 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO95166Q9P278
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.91α = 90
b = 44.75β = 118.54
c = 78.48γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description