7LCZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

SARM1 is a metabolic sensor activated by an increased NMN/NAD + ratio to trigger axon degeneration.

Figley, M.D.Gu, W.Nanson, J.D.Shi, Y.Sasaki, Y.Cunnea, K.Malde, A.K.Jia, X.Luo, Z.Saikot, F.K.Mosaiab, T.Masic, V.Holt, S.Hartley-Tassell, L.McGuinness, H.Y.Manik, M.K.Bosanac, T.Landsberg, M.J.Kerry, P.S.Mobli, M.Hughes, R.O.Milbrandt, J.Kobe, B.DiAntonio, A.Ve, T.

(2021) Neuron 109: 1118

  • DOI: https://doi.org/10.1016/j.neuron.2021.02.009
  • Primary Citation of Related Structures:  
    7LCY, 7LCZ, 7LD0

  • PubMed Abstract: 

    Axon degeneration is a central pathological feature of many neurodegenerative diseases. Sterile alpha and Toll/interleukin-1 receptor motif-containing 1 (SARM1) is a nicotinamide adenine dinucleotide (NAD + )-cleaving enzyme whose activation triggers axon destruction. Loss of the biosynthetic enzyme NMNAT2, which converts nicotinamide mononucleotide (NMN) to NAD + , activates SARM1 via an unknown mechanism. Using structural, biochemical, biophysical, and cellular assays, we demonstrate that SARM1 is activated by an increase in the ratio of NMN to NAD + and show that both metabolites compete for binding to the auto-inhibitory N-terminal armadillo repeat (ARM) domain of SARM1. We report structures of the SARM1 ARM domain bound to NMN and of the homo-octameric SARM1 complex in the absence of ligands. We show that NMN influences the structure of SARM1 and demonstrate via mutagenesis that NMN binding is required for injury-induced SARM1 activation and axon destruction. Hence, SARM1 is a metabolic sensor responding to an increased NMN/NAD + ratio by cleaving residual NAD + , thereby inducing feedforward metabolic catastrophe and axonal demise.


  • Organizational Affiliation

    Department of Developmental Biology, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA; Needleman Center for Neurometabolism and Axonal Therapeutics, Washington University School of Medicine in Saint Louis, St. Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform B of NAD(+) hydrolase sarm1
A, B
309Drosophila 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMN (Subject of Investigation/LOI)
Query on NMN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.921α = 103.516
b = 50.788β = 101.899
c = 76.054γ = 95.261
Software Package:
Software NamePurpose
PHENIXrefinement
autoSHARPphasing
Cootmodel building
BUCCANEERmodel building
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1107804
National Health and Medical Research Council (NHMRC, Australia)Australia1160570
National Health and Medical Research Council (NHMRC, Australia)Australia1071659
National Health and Medical Research Council (NHMRC, Australia)Australia1108859
Australian Research Council (ARC)AustraliaFL180100109
Australian Research Council (ARC)AustraliaDE170100783

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2021-04-21
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references