PXD033748

PXD033748 is an original dataset announced via ProteomeXchange.

Title	Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro (XL-MS)
Description	SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic, entailing enormous disruption worldwide. Its ~30 kb RNA genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro/nsp5). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-10/11 polyprotein, whose mature products are cofactors of the viral replicase, identifying the order of cleavages: 1) nsp9-10, 2) nsp8-9/nsp10-11, and 3) nsp7-8. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and X-ray scattering yielded three-dimensional models of the nsp7-10/11 polyprotein, and the data suggest that the nsp7-10/11 structure in complex with Mpro strongly resembles the unbound polyprotein. Our array of techniques supports the notion that interplay between polyprotein conformation and junction accessibility determine the preference and order of cleavages. Finally, we leveraged assays of limited proteolysis by Mpro of nsp7-11 using a series of inhibitors/binders to characterize Mpro inhibition using a polyprotein substrate.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:31:07.397.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Valentine Courouble
SpeciesList	scientific name: Severe acute respiratory syndrome coronavirus 2; NCBI TaxID: 2697049;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-06 10:45:37	ID requested
1	2022-12-19 11:48:42	announced
2	2023-01-25 13:10:22	announced	2023-01-25: Updated project metadata.
⏵ 3	2023-11-14 08:31:08	announced	2023-11-14: Updated project metadata.

Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E, Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv, 8(49):eadd2191(2022) [pubmed]

ProteomeXchange project tag: Sars-cov-2, Covid-19

submitter keyword: nsp7-8,XL-MS, nsp7-11, Mpro, SARS-CoV-2, polyprotein

Patrick R Griffin
contact affiliation	Professor, Molecular Medicine Scientific Director UF Scripps Biomedical Research University of Florida
contact email	pgriffin@scripps.edu
lab head
Valentine Courouble
contact affiliation	Scripps Research
contact email	vcouroub@scripps.edu
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/2022/12/PXD033748

PRIDE project URI

• PRIDE
  1. PXD033748
     1. Label: PRIDE project
     2. Name: Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro (XL-MS)