PXD060731-1

PXD060731 is an original dataset announced via ProteomeXchange.

Title	UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains
Description	Ubiquitin chains encode signals defining the fates of their modified proteins. Ubiquitin chain-mediated proteasomal degradation is a widespread eukaryotic regulatory mechanism. Yet, heterogeneity of intracellular ubiquitination has precluded systematically comparing degradation capacities of different ubiquitin chains. Here, we monitor cellular degradation and deubiquitination at high temporal resolution after delivery of bespoke ubiquitinated proteins into human cells. Comparing degradation of a model substrate modified with various K48, K63 or K48/K63-branched ubiquitin chains revealed fundamental differences in their intracellular degradation capacities. K48 chains with three or more ubiquitins triggered degradation within minutes. K63-ubiquitinated substrate was rapidly deubiquitinated rather than degraded. Surprisingly, degradation and deubiquitination behaviour of K48/K63-branched chains was determined by the identity of the substrate-anchored chain, establishing that branched chains are not the sum of their parts. Overall, our work reveals a degradation code for ubiquitin chains varying by linkage, length and topology and a functional hierarchy within branched ubiquitin chains.
HostingRepository	PRIDE
AnnounceDate	2025-06-23
AnnouncementXML	Submission_2025-06-22_16:08:36.857.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbara Steigenberger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-12 09:46:42	ID requested
⏵ 1	2025-06-22 16:08:37	announced

10.1016/j.molcel.2025.02.021;

Kiss L, James LC, Schulman BA, UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains. Mol Cell, 85(7):1467-1476.e6(2025) [pubmed]

submitter keyword: Ubiquitin, K48, deubiquitination, K63, protein degradation, proteasome, proteostasis, electroporation, ubiquitin code, branched ubiquitin chains

Leo Kiss
contact affiliation	Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
contact email	lkiss@biochem.mpg.de
lab head
Barbara Steigenberger
contact affiliation	MPI of Biochemistry
contact email	steigenberger@biochem.mpg.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/2025/06/PXD060731

PRIDE project URI

• PRIDE
  1. PXD060731
     1. Label: PRIDE project
     2. Name: UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains