ISDA: 8GQ5

Deposition Date 2022-08-29

Release Date 2023-01-18

Last Version Date 2024-11-13

Entry Detail

PDB ID:

8GQ5

Keywords:

HYDROLASE

Title:

Human SARM1 bounded with NMN and Nanobody-C6, double-layer structure

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)
Vicugna pacos (Taxon ID: 30538)

Expression System(s):

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.70 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:NAD(+) hydrolase SARM1
Gene (Uniprot):SARM1
Chain IDs:A, C (auth: B), E (auth: C), G (auth: D), I (auth: E), K (auth: F), M (auth: G), O (auth: H), Q (auth: I), S (auth: J), U (auth: K), W (auth: L), Y (auth: M), AA (auth: N), CA (auth: O), EA (auth: P)
Chain Length:119
Number of Molecules:16
Biological Source:Homo sapiens

UniProt ID:Q6SZW1 Pfam ID:PF07647, PF13676

Polymer Type:polypeptide(L)
Molecule:Nanobody C6
Chain IDs:B (auth: a), D (auth: b), F (auth: c), H (auth: d), J (auth: e), L (auth: f), N (auth: g), P (auth: h), R (auth: i), T (auth: j), V (auth: k), X (auth: l), Z (auth: m), BA (auth: n), DA (auth: o), FA (auth: p)
Chain Length:119
Number of Molecules:16
Biological Source:Vicugna pacos

Ligand Molecules

Primary Citation

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.Show

Nat Commun 13 7898 7898 (2022)

PMID: 36550129 DOI: 10.1038/s41467-022-35581-y

Abstact

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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Primary Citation of related structures

Abstact

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