9UGJ | pdb_00009ugj

Structure of SARM1 bound to SIR3-ADPR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9UGJ

This is version 1.1 of the entry. See complete history

Literature

SARM1 activation promotes axonal degeneration via a two-step phase transition.

Zhang, W.Zhou, Q.Zhang, J.Wang, J.Wu, Q.Zheng, S.Wang, X.

(2026) Nat Chem Biol 22: 435-445

  • DOI: https://doi.org/10.1038/s41589-025-02009-9
  • Primary Citation Related Structures: 
    9UGJ

  • PubMed Abstract: 

    SARM1 is a key executioner of axonal degeneration, acting through NAD⁺ depletion by NADase activity of its TIR domain. Although normally autoinhibited, SARM1 becomes activated in response to axonal damage; however, the underlying mechanism remains unclear. Here, using a class of pyridine-containing compounds that trigger SARM1-dependent axon degeneration, we uncover a two-step activation process. First, NMN primes the base exchange activity of SARM1, generating covalent adducts between ADP-ribose (an NAD⁺ hydrolysis product) and the compounds. These ADP-ribose conjugates then serve as molecular glues to promote the assembly of superhelical SARM1 filaments, in which TIR domains adopt an active configuration. After reaching solubility limits, these filaments condense into stable, phase-separated assemblies with full enzymatic activity. Unexpectedly, several clinical-stage SARM1 inhibitors targeting its TIR domain also form such adducts, paradoxically promoting its activation. These findings reveal a molecular mechanism that spatially restricts SARM1 activation to damaged axons and offer new guidance for therapeutic strategies targeting SARM1.


  • Organizational Affiliation
    • Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 677.67 kDa 
  • Atom Count: 8,542 
  • Modeled Residue Count: 1,106 
  • Deposited Residue Count: 6,088 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD(+) hydrolase SARM1
A, B, C, D, E
A, B, C, D, E, F, G, H
761Homo sapiensMutation(s): 0 
Gene Names: SARM1KIAA0524SAMD2SARM
EC: 3.2.2.6 (PDB Primary Data), 3.2.2 (PDB Primary Data)
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
A1EO4
(Subject of Investigation/LOI)

Query on A1EO4



Download:Ideal Coordinates CCD File
I [auth B]
J [auth C]
K [auth D]
L [auth E]
M [auth E]
I [auth B],
J [auth C],
K [auth D],
L [auth E],
M [auth E],
N [auth F],
O [auth H],
P [auth H]
[[(2~{S},3~{R},4~{S},5~{S})-5-(4-azanylimidazo[4,5-d]pyridazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-[4-methyl-3-(2-oxidanylidene-3~{H}-1,3-benzoxazol-6-yl)pyridin-1-ium-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C28 H32 N7 O15 P2
GTUDWLPAEYWLMM-SVANQVPXSA-O

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Data collection, Database references