PXD064931-1

PXD064931 is an original dataset announced via ProteomeXchange.

Title	Cross-link MS analysis of human 26S proteasome in complex with RPN13:UCHL5 (without substrate).
Description	This project investigates how the human 26S proteasome recognizes and processes proteins tagged with K11/K48-branched ubiquitin chains, which signal for rapid degradation during cell cycle progression and proteotoxic stress. Using cryo-electron microscopy (cryo-EM), the study uncovers a novel K11-linked ubiquitin binding site at the interface of RPN2 and RPN10, alongside known K48-specific sites. Structural insights reveal how these branched ubiquitin chains are preferentially recognized, enhancing proteasomal degradation efficiency. Complementary cross-linking mass spectrometry (XL-MS) identifies transient interactions between RPN13, RPN2, RPN10, and core proteasome subunits, further elucidating the dynamic coordination within the proteasome during substrate processing.
HostingRepository	PRIDE
AnnounceDate	2025-09-22
AnnouncementXML	Submission_2025-09-22_05:48:35.613.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Piotr Draczkowski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-12 05:24:29	ID requested
⏵ 1	2025-09-22 05:48:36	announced

Dataset with its publication pending

submitter keyword: RPN13, proteasome, UCHL5,26S

Shang-Te Danny Hsu
contact affiliation	Institute of Biological Chemistry, Academia Sinica, Taipei, 115201, Taiwan Institute of Biochemical Sciences, National Taiwan University, Taipei, 106319, Taiwan International Institute for Sustainability with Knotted Chiral Meta Matter (SKCM2), Hiroshima University, Hiroshima, 739-8511, Japan
contact email	sthsu@gate.sinica.edu.tw
lab head
Piotr Draczkowski
contact affiliation	SciLifeLab
contact email	piotr.draczkowski@scilifelab.se
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/2025/09/PXD064931

PRIDE project URI

• PRIDE
  1. PXD064931
     1. Label: PRIDE project
     2. Name: Cross-link MS analysis of human 26S proteasome in complex with RPN13:UCHL5 (without substrate).