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ProteomicsDiscovery and characterization of ZUFSP, a novel DUB class important for genome stability
Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and cataly...
ORGANISM(S): Homo sapiens (Human) 
2018-10-22 | PXD008509 | Pride
Ubiquitin binding domain Deubiquitinase Dna damage 
ProteomicsHuman UFSP1 is an active protease that regulates UFM1 maturation and UFMylation
An essential first step in the posttranslational modification of proteins with UFM1, UFMylation, is the proteolytic cleavage of pro-UFM1 to expose a C-terminal glycine. Of the two UFM1-specific proteases (UFSPs) identified in humans, only UFSP2 is reported to be active since the annotated sequence o...
ORGANISM(S): Homo sapiens (Human) 
2022-08-22 | PXD035142 | Pride
Ribosome Ufm1 Endoplasmic reticulum (er) Cysteine protease Ubiquitin like modifier 
ProteomicsSystematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
Please refer to the manuscript for a detailed description.
ORGANISM(S): Homo sapiens (Human) 
2026-03-19 | PXD068553 | Pride
Dubs Slim Cyld Phage display Usp11 Usp22 Usp33 Usp20 
ProteomicsExpansion of DUB functionality by alternative isoforms: USP35, a case study
Protein ubiquitylation is a dynamic post-translational modification that can be reversed by deubiquitylating enzymes (DUBs). It is unclear how the small number of ~100 DUBs present in mammalian cells regulates the thousands of different ubiquitylation events. Here we analysed annotated transcripts o...
ORGANISM(S): Homo sapiens (Human) 
2018-04-27 | PXD009286 | Pride
Endoplasmic reticulum Apoptosis Deubiquitinase Lipid droplets Ubiquitin signalling 
ProteomicsFAF1 and FAF2 enhance human p97-UFD1-NPL4 complex unfoldase activity enabling rational design of p97 activators - Crosslinking mass spec data
VCP/p97 is an AAA+ ATPase that, together with its cofactors UFD1-NPL4 (p97-UN), binds and unfolds ubiquitylated substrates to maintain cellular homeostasis. The human p97-UN complex associates with additional cofactors, but how these cofactors modulate p97-UN activity is not fully understood. We scr...
ORGANISM(S): Homo sapiens (Human) 
2026-07-28 | PXD078865 | Pride
Atpase Xl-ms Faf2 Ufd1 Vcp Npl4 P97 
ProteomicsLC-MS/MS analysis of ribosome UFMylation in vitro
UFMylation, is a Ubiquitin-like modification occurring on RPL26, a ribosomal subunit, upon ribosome stalling at the ER membrane. This modification is achieved by a pool of enzymes commonly referred to as E1-activating, E2-conjugating and E3-ligase enzymes. The UFM1 E3 ligase comprises of three prote...
ORGANISM(S): Homo sapiens (Human) 
2024-03-22 | PXD046991 | Pride
In vitro reconstitution Rpl26 ufmylation Ribosome ufmylation 
ProteomicsBiochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies
Of 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 proteas...
ORGANISM(S): Homo sapiens (Human) 
2021-09-15 | PXD022904 | Pride
Ubiqutylation Isg15 Sars cov-2 
ProteomicsK48-K63-Ubiquitin chain pulldown from U2OS cell lysates
SpyTagged branched and unbranched K48- and K63-linked Tetra-Ubiquitin chains were immobilized on SpyCatcher agarose (48Ub4; 63Ub4; [Ub]2-48,63Ub-48Ub; [Ub]2-48,63Ub-63Ub). Pulldown were performed from protease-inhibitor treated U2OS cell lines to identify specific binders of K48-K63-branched Ub4.
ORGANISM(S): Homo sapiens (Human) 
2024-05-07 | PXD046025 | Pride
Human Lc-msms Dia Ubiquitin Branched ubiquitin 
ProteomicsUFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
Supporting MS data for paper (doi: 10.1038/s41586-024-07073-0) by DaRosa P.A., Penchev I. et al., titled "UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER". Index of MS supporting files uploaded: Related to Related to Fig. 1b, c (xb01004(UFM1), xb01005(SBP-UFM1): LFQ IP-MS (Un...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-12-22 | MSV000093721 | MassIVE
ProteomicsUFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER
Supporting MS data for paper (doi: 10.1038/s41586-024-07073-0) by DaRosa P.A., Penchev I. et al., titled "UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER". Index of MS supporting files uploaded: - Related to Fig. 1a and Extended Data Fig. 1a (AO3435-AO3440: TMT proteomics (Un...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-11-27 | MSV000093510 | MassIVE
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