8GNI | pdb_00008gni

Human SARM1 bounded with NMN and Nanobody-C6, Conformation 1

• PDB DOI: https://doi.org/10.2210/pdb8GNI/pdb
• EM Map EMD-34165: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Vicugna pacos
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-08-24 Released: 2023-01-18 
• Deposition Author(s): Cai, Y., Zhang, H.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

A conformation-specific nanobody targeting the nicotinamide mononucleotide-activated state of SARM1.

Hou, Y.N., Cai, Y., Li, W.H., He, W.M., Zhao, Z.Y., Zhu, W.J., Wang, Q., Mai, X., Liu, J., Lee, H.C., Stjepanovic, G., Zhang, H., Zhao, Y.J.

(2022) Nat Commun 13: 7898-7898

• PubMed: 36550129 
• DOI: https://doi.org/10.1038/s41467-022-35581-y
• Primary Citation Related Structures: 
  8GNI, 8GNJ, 8GQ5


• PubMed Abstract: 
  

  Sterile alpha (SAM) and Toll/interleukin-1 receptor (TIR) motif containing 1 (SARM1) is an autoinhibitory NAD-consuming enzyme that is activated by the accumulation of nicotinamide mononucleotide (NMN) during axonal injury. Its activation mechanism is not fully understood. Here, we generate a nanobody, Nb-C6, that specifically recognizes NMN-activated SARM1. Nb-C6 stains only the activated SARM1 in cells stimulated with CZ-48, a permeant mimetic of NMN, and partially activates SARM1 in vitro and in cells. Cryo-EM of NMN/SARM1/Nb-C6 complex shows an octameric structure with ARM domains bending significantly inward and swinging out together with TIR domains. Nb-C6 binds to SAM domain of the activated SARM1 and stabilized its ARM domain. Mass spectrometry analyses indicate that the activated SARM1 in solution is highly dynamic and that the neighboring TIRs form transient dimers via the surface close to one BB loop. We show that Nb-C6 is a valuable tool for studies of SARM1 activation.

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Organizational Affiliation: 
• State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China.
Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China.
Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China. [e-mail].
Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. [e-mail].
State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. [e-mail].
Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 172.48 kDa 
• Atom Count: 5,832 
• Modeled Residue Count: 746 
• Deposited Residue Count: 1,567 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(+) hydrolase SARM1	A, B	724	Homo sapiens	Mutation(s): 0  Gene Names: SARM1, KIAA0524, SAMD2, SARM 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody C6	C	119	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMN (Subject of Investigation/LOI)	D [auth A]	BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE C11 H16 N2 O8 P DAYLJWODMCOQEW-TURQNECASA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16
RECONSTRUCTION	RELION	3.1.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Cai, Y., Zhang, H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Refinement description, Structure summary