9L9I | pdb_00009l9i

Crystal structure of ARMS 1-4 ARs in complex with GABARAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.240 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A non-canonical ARMS-GABARAP interaction modulates dendritic spine formation and synaptic development.

Jiang, W.Ye, J.Chen, J.Wang, X.Li, Y.Li, J.Mei, Y.Lyu, Y.Hu, W.Wang, C.

(2026) EMBO J 

  • DOI: https://doi.org/10.1038/s44318-025-00669-w
  • Primary Citation of Related Structures:  
    9L9I

  • PubMed Abstract: 

    ARMS (ankyrin repeat-rich membrane spanning) is a scaffold protein essential for neurotrophic signaling, synaptic development, and cytoskeletal remodeling. Despite its central role in neuronal function, how ARMS is regulated at the molecular level remains poorly understood. Here, we identify GABARAP, an Atg8-family autophagy adaptor, as a novel ARMS-binding protein that directly interacts with its N-terminal ankyrin repeats. We present the crystal structure of the ARMS-GABARAP complex, revealing an atypical interaction mode distinct from canonical LIR-dependent Atg8 interactions. Remarkably, ARMS specifically binds to the GABARAP subfamily of Atg8 proteins, setting it apart from the LC3 subfamily. Functional analysis demonstrates that GABARAP negatively regulates ARMS-mediated dendritic spine development and maturation in hippocampal neurons. Additionally, disrupting the ARMS-GABARAP complex using ankyrin-derived peptides alters ARMS subcellular localization, increasing its accumulation in the soma of neurons. Collectively, our findings uncover a novel ARMS-GABARAP interaction mechanism, establish the regulatory role of this complex in neuronal protein homeostasis, and suggest potential therapeutic strategies for targeting scaffold protein interactions in neurodevelopmental and neurodegenerative disorders.


  • Organizational Affiliation
    • Department of Neurology, the First Affiliated Hospital of USTC, Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinase D-interacting substrate of 220 kDa,Gamma-aminobutyric acid receptor-associated protein259Rattus norvegicusMutation(s): 0 
Gene Names: Kidins220ArmsGabarap
UniProt
Find proteins for P60517 (Rattus norvegicus)
Explore P60517 
Go to UniProtKB:  P60517
Find proteins for Q9EQG6 (Rattus norvegicus)
Explore Q9EQG6 
Go to UniProtKB:  Q9EQG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9EQG6P60517
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.240 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.954α = 90
b = 58.31β = 90
c = 92.649γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Database references