PXD075114-1

PXD075114 is an original dataset announced via ProteomeXchange.

Title	Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry
Description	The 26S proteasome is the endpoint of the ubiquitin-proteasome system, an essential pathway for maintaining cellular homeostasis through targeted degradation of misfolded, damaged, and obsolete proteins. Substrates labeled with ubiquitin are directed to the 26S proteasome by binding to one or more ubiquitin receptors. However, ubiquitin-dependent degradation occurs even when the canonical receptor sites are mutated, suggesting the presence of additional, unidentified binding sites. Here we created photo-crosslinkable probes for ubiquitin interactions by incorporating the unnatural amino acid p-benzoyl-L-phenylalanine into ubiquitin. We show that these probes can be used to measure apparent affinities for known receptors and to reveal novel ubiquitin-binding sites on the yeast 26S proteasome. Through photo-crosslinking mass-spectrometry experiments we identified a groove on the top of the proteasome, formed by Rpn2, Rpn9, Rpn10, and Rpn12, that serves as an additional ubiquitin-binding interface. Our photo-crosslinkable probes thus serve as versatile tools for the characterization of ubiquitin-protein interactions and the identification of ubiquitin-binding domains.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_16:09:43.655.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ken Dong
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-02 17:02:48	ID requested
⏵ 1	2026-06-07 16:09:44	announced

10.1016/j.jbc.2026.111481;

MacRae NS, Dong KC, Harimoto H, Martin A, Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry. J Biol Chem, 302(6):111481(2026) [pubmed]

submitter keyword: 26S Proteasome, Ubiquitin, Ubiquitin Receptors

Andreas Martin
contact affiliation	Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720 USA California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720 Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720 USA
contact email	a.martin@berkeley.edu
lab head
Ken Dong
contact affiliation	Howard Hughes Medical Institute/ UC Berkeley
contact email	k77dong@berkeley.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD075114
     1. Label: PRIDE project
     2. Name: Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry