7NAJ

Crystal structure of the TIR domain from human SARM1 in complex with ara-2'F-ADPR

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2021-06-21 Released: 2022-03-23 
  • Deposition Author(s): Shi, Y., Ve, T.
  • Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of SARM1 activation, substrate recognition, and inhibition by small molecules.

Shi, Y.Kerry, P.S.Nanson, J.D.Bosanac, T.Sasaki, Y.Krauss, R.Saikot, F.K.Adams, S.E.Mosaiab, T.Masic, V.Mao, X.Rose, F.Vasquez, E.Furrer, M.Cunnea, K.Brearley, A.Gu, W.Luo, Z.Brillault, L.Landsberg, M.J.DiAntonio, A.Kobe, B.Milbrandt, J.Hughes, R.O.Ve, T.

(2022) Mol Cell 82: 1643

  • DOI: https://doi.org/10.1016/j.molcel.2022.03.007
  • Primary Citation of Related Structures:  
    7NAG, 7NAH, 7NAI, 7NAJ, 7NAK, 7NAL

  • PubMed Abstract: 

    The NADase SARM1 (sterile alpha and TIR motif containing 1) is a key executioner of axon degeneration and a therapeutic target for several neurodegenerative conditions. We show that a potent SARM1 inhibitor undergoes base exchange with the nicotinamide moiety of nicotinamide adenine dinucleotide (NAD + ) to produce the bona fide inhibitor 1AD. We report structures of SARM1 in complex with 1AD, NAD + mimetics and the allosteric activator nicotinamide mononucleotide (NMN). NMN binding triggers reorientation of the armadillo repeat (ARM) domains, which disrupts ARM:TIR interactions and leads to formation of a two-stranded TIR domain assembly. The active site spans two molecules in these assemblies, explaining the requirement of TIR domain self-association for NADase activity and axon degeneration. Our results reveal the mechanisms of SARM1 activation and substrate binding, providing rational avenues for the design of new therapeutics targeting SARM1.


  • Organizational Affiliation

    Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sterile alpha and TIR motif-containing protein 1
A, B
144Homo sapiensMutation(s): 0 
Gene Names: SARM1KIAA0524SAMD2SARM
UniProt & NIH Common Fund Data Resources
Find proteins for Q6SZW1 (Homo sapiens)
Explore Q6SZW1 
Go to UniProtKB:  Q6SZW1
PHAROS:  Q6SZW1
GTEx:  ENSG00000004139 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6SZW1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1LK (Subject of Investigation/LOI)
Query on 1LK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1,4-anhydro-2-deoxy-2-fluoro-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-D-arabinitol
C5 H11 F O9 P2
JLUFHMADAUUBBV-WDCZJNDASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.511α = 90
b = 117.063β = 90
c = 33.043γ = 90
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

  • Released Date: 2022-03-23 
  • Deposition Author(s): Shi, Y., Ve, T.

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

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2022-05-18
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description