PXD049043

PXD049043 is an original dataset announced via ProteomeXchange.

Title	Structural basis of PROTAC-induced target ubiquitination mechanism - identification of BRD4 ubiquitination sites
Description	Proteolysis Targeting Chimeras (PROTACs) hijack the ubiquitin proteasome system to ubiquitinate target proteins, targeting them for degradation by the proteasome. An understudied process that is essential to the PROTAC mechanism of action is ubiquitination of the target protein and ubiquitin (Ub) chain elongation. To elucidate the mechanism of PROTAC-induced ubiquitination of BRD4(BD2) ubiquitination sites on Brd4BD2 were mapped by mass spectrometry following an in vitro ubiquitination assay containing neddylated-CRL2VHL, Brd4BD2, MZ1, Uba1 and either UBE2R1 or UBE2D2. Time points were taken at 0 minutes, 10 minutes, 0.5 hours, 1 hour and 3 hours. Proteins were separated by SDS-page analysis. To visualize proteins the gel was stained with Coomassie blue and gel slices containing ubiquitin modified Brd4BD2 across timepoints and increasing molecular weight were excised from the gel and were analyzed by mass spectrometry. To identify sites of ubiquitination a search for GG-K peptides was performed in MaxQuant. Based on existing structures the modified lysine residues were all situated on the same face of BD2.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_12:54:45.888.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sarah Chandler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-31 06:27:10	ID requested
⏵ 1	2025-05-06 12:54:46	announced

Crowe C, Nakasone MA, Chandler S, Craigon C, Sathe G, Tatham MH, Makukhin N, Hay RT, Ciulli A, Mechanism of degrader-targeted protein ubiquitinability. Sci Adv, 10(41):eado6492(2024) [pubmed]

10.1126/sciadv.ado6492;

submitter keyword: PROTAC, MZ1, Ubiquitin, CRL2VHL,BRD4

Ronald T Hay
contact affiliation	University of Dundee, School of Life Sciences, Department of molecular, cellular and developmental biology
contact email	r.t.hay@dundee.ac.uk
lab head
Sarah Chandler
contact affiliation	University of Dundee
contact email	2431160@dundee.ac.uk
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/2025/05/PXD049043

PRIDE project URI

• PRIDE
  1. PXD049043
     1. Label: PRIDE project
     2. Name: Structural basis of PROTAC-induced target ubiquitination mechanism - identification of BRD4 ubiquitination sites