PXD049009

PXD049009 is an original dataset announced via ProteomeXchange.

Title	The kinetics of nsp7-11 polyprotein processing and impact on complexation with nsp16 among human coronaviruses
Description	In coronavirus (CoV) infection, polyproteins (pp1a/pp1ab) are processed into non-structural proteins (nsps), which largely form the replication/transcription complex (RTC). The polyprotein processing and complex formation is critical and offers potential therapeutic targets. However, the interplay of polyprotein processing and RTC-assembly remains poorly understood. Here, we studied two key aspects: The order of polyprotein processing by viral main protease Mpro and its influence on complex formation with the methyltransferase nsp16. Moreover, we established an approach to determine rate constants k from cleavage sites in structured CoV polyprotein based on native mass spectrometry (MS). The high sensitivity and precision of our method allowed quantification of multi-reaction kinetics of nsp7-11 processing from four human pathogenic CoV species. The experimentally determined rate constants are put into perspective with a comprehensive analysis of primary sequences and structural models, revealing distinct cleavage mechanisms for each site based on their local structural environments. Our systematic approach provides a blueprint for kinetic analysis of complex multi-cleavage reactions.
HostingRepository	PRIDE
AnnounceDate	2025-07-08
AnnouncementXML	Submission_2025-07-08_14:24:41.610.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kira Schamoni-Kast
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Q-Tof Ultima; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-30 06:51:41	ID requested
⏵ 1	2025-07-08 14:24:41	announced

10.1038/S41467-025-61554-Y;

submitter keyword: mass spectrometry, SARS-CoV-2,Kinetics, native MS, rate constants, complexation

Charlotte Uetrecht
contact affiliation	CSSB Centre for Structural Systems Biology, Deutsches Elektronen Synchroton DESY, Leibniz Institute of Virology, Germany; University of Luebeck, Institute for Chemistry and Metabolomics
contact email	charlotte.uetrecht@cssb-hamburg.de
lab head
Kira Schamoni-Kast
contact affiliation	Centre for Structural Systems Biology (CSSB), Leibniz Institute of Virology (LIV)
contact email	kira.schamoni-kast@cssb-hamburg.de
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/PXD049009

PRIDE project URI

• PRIDE
  1. PXD049009
     1. Label: PRIDE project
     2. Name: The kinetics of nsp7-11 polyprotein processing and impact on complexation with nsp16 among human coronaviruses