PXD033528 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | A Conformation specific Nanobody Targeting the NMN-activated State of SARM1 |
Description | Upon axonal injury, Sterile alpha (SAM) and Toll/interleukin-1 receptor (TIR) motif containing 1 (SARM1) is activated by nicotinamide mononucleotide (NMN) to deplete NAD and consequently promote the process of axon degeneration (AxD). Currently, only the inactive form of SARM1 in its auto-inhibitory conformation has been resolved. The flexibility of the enzymatically active form of SARM1 has so far precluded its structural determination. To solve the problem, we generated a stabilizing nanobody, Nb-C6, that specifically recognized 30 only the NMN-activated form of SARM1. The conformation specificity was verified by immunoprecipitation and surface plasmon resonance. Fluorescently labeled Nb-C6 could immunostain only the activated SARM1 in cells stimulated with CZ-48, a permeant mimetic of NMN. Expression of Nb-C6 in live cells resulted in stabilization of the active form of the endogenous and exogenous SARM1, producing and elevating cellular levels of cyclic ADP-ribose, a calcium messenger. Cryo-EM of the NMN-activated SARM1 complexed by Nb-C6 showed an octameric structure resembling a “blooming lotus” with the ARM domains bending significantly inward and swinging out together with the TIR domains to form the “petals of the lotus”. Nb-C6 bound to the SAM domain of the activated SARM1 and stabilized its Armadillo repeat motif domain. Analyses using hydrogen-deuterium exchange mass spectrometry (HDX-MS), and cross-linking MS (XL-MS) indicate that the activated SARM1 is highly dynamic and flexible and the neighboring TIRs form dimers via the surface close to one BB loop. The Nanobody is thus a valuable tool for delineating the mechanism of activation of SARM1 in AxD and other cellular processes. |
HostingRepository | PRIDE |
AnnounceDate | 2022-11-29 |
AnnouncementXML | Submission_2022-11-29_05:18:55.092.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | GoranStjepanovic |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Orbitrap Eclipse |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-04-28 01:36:23 | ID requested | |
⏵ 1 | 2022-11-29 05:18:55 | announced | |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: SARM1, ADP ribosyl cyclase, XL-MS, HDX-MS |
Contact List
GoranStjepanovic |
contact affiliation | Kobilka Institute of Innovative Drug Discovery, School ofMedicine, The Chinese University of Hong Kong, Shenzhen, China, 518172 |
contact email | goranstjepanovic@cuhk.edu.cn |
lab head | |
GoranStjepanovic |
contact affiliation | CUHKSZ |
contact email | goranstjepanovic@cuhk.edu.cn |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/11/PXD033528 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD033528
- Label: PRIDE project
- Name: A Conformation specific Nanobody Targeting the NMN-activated State of SARM1