PXD052584-1

PXD052584 is an original dataset announced via ProteomeXchange.

Title	Cross-linking MS supporting: Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome
Description	The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. However, the inherent disorder of full-length N has hampered its structural analysis. Here, we describe a stepwise method using viral-derived RNAs to stabilize SARS-CoV-2 N for EM analysis. We identified pieces of RNA from the SARS-CoV-2 genome that promote the formation of structurally homogeneous N dimers, intermediates of assembly, and filamentous capsid-like structures. Building on these results, we engineered a symmetric RNA to stabilize N protein dimers, the building block of high-order assemblies, for EM analyses. We combined domain-specific monoclonal antibodies against N with chemical cross-linking mass spectrometry and cryo-EM to validate the atomic model for the N dimer. The resulting N dimer structure provides insights into its architectural and antigenic principles, which can guide design of pan-coronavirus therapeutics.
HostingRepository	PRIDE
AnnounceDate	2025-07-21
AnnouncementXML	Submission_2025-07-20_16:06:59.842.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD052584
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andrew Norris
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-27 03:35:30	ID requested
⏵ 1	2025-07-20 16:07:00	announced

10.1038/s41467-025-61861-4;

10.6019/PXD052584;

Landeras-Bueno S, Hariharan C, Avalos RD, Norris AS, Snyder DT, Hastie KM, Harkins S, Zandonatti M, Rajamanickam RR, Olmedillas E, Miller R, Shresta S, Wysocki VH, Saphire EO, Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome fragment. Nat Commun, 16(1):6521(2025) [pubmed]

submitter keyword: cross-linking,XL-MS, SARS-CoV-2 N

Vicki H. Wysocki
contact affiliation	Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 14 43210, USA
contact email	wysocki.11@osu.edu
lab head
Andrew Norris
contact affiliation	The Ohio State University
contact email	norris942@gmail.com
dataset submitter

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/2025/07/PXD052584

PRIDE project URI

• PRIDE
  1. PXD052584
     1. Label: PRIDE project
     2. Name: Cross-linking MS supporting: Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome