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PXD022904 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleBiochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies
DescriptionOf the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging to characterize. Encoded within the multidomain Nsp3 is the papain-like protease PLpro that cleaves not only the viral protein but also polyubiquitin and the ubiquitin-like modifier ISG15 from host cells. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal PLpro. Using a MALDI-TOF based assay, we screen 7538 approved clinical compounds and identify five compounds that inhibit PLpro. Despite their ability to inhibit PLpro with IC50s in the low micromolar range, the inhibitors do not have any appreciable antiviral activity in cellular SARS-CoV2 infection assays. We therefore engineered nanobodies that bind to the S1 site of PLpro with nanomolar affinity and inhibit the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRaja Sekhar Nirujogi
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-12-04 00:39:02ID requested
12021-09-15 07:41:15announced
Publication List
Armstrong LA, Lange SM, Dee Cesare V, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y, Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One, 16(7):e0253364(2021) [pubmed]
Keyword List
ProteomeXchange project tag: Sars-cov-2, Covid-19
submitter keyword: SARS CoV-2, ISG15, Ubiqutylation
Contact List
Yogesh Kulathu
contact affiliationMRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
contact emaily.kulathu@dundee.ac.uk
lab head
Raja Sekhar Nirujogi
contact affiliationMRC Protein Phosphorylation Unit, university of Dundee
contact emailrnirujogi@dundee.ac.uk
dataset submitter
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