9L2E | pdb_00009l2e

Structure of SARM1 bound to M1 in the intermediate state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Stepwise activation of SARM1 for cell death and axon degeneration revealed by a biosynthetic NMN mimic.

Huang, Y.Zhang, J.Zhang, W.Chen, J.Chen, S.Wu, Q.Zheng, S.Wang, X.

(2025) Proc Natl Acad Sci U S A 122: e2424906122-e2424906122

  • DOI: https://doi.org/10.1073/pnas.2424906122
  • Primary Citation of Related Structures:  
    9L2D, 9L2E, 9L2F, 9L2G

  • PubMed Abstract: 

    Axon degeneration, driven by the NAD + hydrolyzing enzyme SARM1, is an early pathological hallmark of numerous neurodegenerative diseases. SARM1 exists in an inactive form and is activated following nerve injury. However, the precise molecular mechanism underlying SARM1 activation remains to be fully elucidated. In this study, we report the identification of a potent proactivator of SARM1, G10, which is converted into a direct activator (M1) by the enzyme nicotinamide phosphoribosyltransferase. Cryoelectron microscopy structures of SARM1 bound to M1, as well as to M1 and a nonhydrolyzable NAD + analog (1AD), captured two intermediate activation states and the fully active state, revealing a stepwise mechanism of SARM1 activation. Further, introducing a disulfide bond to prevent conformational transitions between the two intermediate states mediated by M1 stabilized SARM1 in its inactive form and blocked M1-induced cell death. Together, these findings propose a sequential, stepwise activation model for SARM1 and offer a framework for developing potential SARM1 inhibitors for the treatment of neurodegenerative diseases.


  • Organizational Affiliation
    • Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 10094, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(+) hydrolase SARM1
A, B, C, D, E
A, B, C, D, E, F, G, H
732Homo 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19_4092

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: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references