7M6K

Crystal structure of the ARM domain from Drosophila SARM1 in complex with VMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Neurotoxin-mediated potent activation of the axon degeneration regulator SARM1.

Loreto, A.Angeletti, C.Gu, W.Osborne, A.Nieuwenhuis, B.Gilley, J.Merlini, E.Arthur-Farraj, P.Amici, A.Luo, Z.Hartley-Tassell, L.Ve, T.Desrochers, L.M.Wang, Q.Kobe, B.Orsomando, G.Coleman, M.P.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.72823
  • Primary Citation of Related Structures:  
    7M6K

  • PubMed Abstract: 

    Axon loss underlies symptom onset and progression in many neurodegenerative disorders. Axon degeneration in injury and disease is promoted by activation of the NAD-consuming enzyme SARM1. Here, we report a novel activator of SARM1, a metabolite of the pesticide and neurotoxin vacor. Removal of SARM1 completely rescues mouse neurons from vacor-induced neuron and axon death in vitro and in vivo. We present the crystal structure of the Drosophila SARM1 regulatory domain complexed with this activator, the vacor metabolite VMN, which as the most potent activator yet known is likely to support drug development for human SARM1 and NMNAT2 disorders. This study indicates the mechanism of neurotoxicity and pesticide action by vacor, raises important questions about other pyridines in wider use today, provides important new tools for drug discovery, and demonstrates that removing SARM1 can robustly block programmed axon death induced by toxicity as well as genetic mutation.


  • Organizational Affiliation

    John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform B of NAD(+) hydrolase sarm1
A, B
310Drosophila melanogasterMutation(s): 0 
Gene Names: SarmEct4CG43119
EC: 3.2.2.6
UniProt
Find proteins for Q6IDD9 (Drosophila melanogaster)
Explore Q6IDD9 
Go to UniProtKB:  Q6IDD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IDD9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.065α = 103.492
b = 51.01β = 101.784
c = 76.56γ = 96.071
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1160570
Australian Research Council (ARC)AustraliaFL180100109

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description