PXD056954-1

PXD056954 is an original dataset announced via ProteomeXchange.

Title	Streptavidin biotin-CCW16 pulldown to determine CCW16-modified proteins in HeLa lysate
Description	The SUMO-targeted E3 ubiquitin ligase RNF4 plays an important role in safeguarding genome and proteome integrity. RNF4 recognizes polySUMO modified proteins and induces their proteolytic or non-proteolytic ubiquitylation. Based on the key functions of RNF4 maintaining proteome and genome stability, control of DNA damage response and DNA-protein crosslink repair, we explored its role in cancer cell survival and as a potential drug target. We found that RNF4 is overexpressed in acute myeloid leukemia and expression levels correlate with poor survival. To develop PROTACs for targeted degradation of RNF4, we aimed to exploit the recently developed cysteine-reactive RNF4 ligand CCW16, and synthesized a set of CCW16-derived degrader molecules using established VHL- and CRBN E3 ligands. To determine CCW16 specificity and binding partners, we performed a Streptavidin Biotin-CCW16 pull down of HeLa cell lysate. We detected around 2000 proteins, which showed significant increase in binding to CCW16 biotin, compared to Biotin only. Interestingly, we found proteins of the peroxiredoxin family covalently modified with CCW16 at the catalytically active cysteine residues, indicating an induction of oxidative stress.
HostingRepository	PRIDE
AnnounceDate	2025-08-21
AnnouncementXML	Submission_2025-08-21_05:49:21.779.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Stefan Müller
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-18 08:46:41	ID requested
⏵ 1	2025-08-21 05:49:22	announced

Dataset with its publication pending

submitter keyword: CCW16, targets, HeLa, LFQ,RNF4

Stefan Müller
contact affiliation	Institute of Biochemistry II, Goethe University Frankfurt,Medical Faculty, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
contact email	ste.mueller@em.uni-frankfurt.de
lab head
Stefan Müller
contact affiliation	Institute of Biochemistry II University Hospital Building 75 Theodor-Stern-Kai 7 60590 Frankfurt (Main)
contact email	ag-mueller@gmx.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/2025/08/PXD056954

PRIDE project URI

• PRIDE
  1. PXD056954
     1. Label: PRIDE project
     2. Name: Streptavidin biotin-CCW16 pulldown to determine CCW16-modified proteins in HeLa lysate