PXD067015

PXD067015 is an original dataset announced via ProteomeXchange.

Title	Multi-scale classification decodes the complexity of the human E3 ligome
Description	E3 ubiquitin ligases are key regulators of protein homeostasis, targeting specific proteins for degradation via the ubiquitin-proteasome system (UPS). They provide crucial substrate specificity, making them promising candidates for the design of novel therapeutics. This work presents a comprehensive, annotated dataset of high-confidence catalytic human E3 ligases, termed the “E3 ligome”. Integrating disparate data from various granularity layers, including protein sequence, domain architecture, 3D structure, function, localization, and expression, we learn an emergent distance metric, capturing authentic relationships within this heterogeneous group. A weakly-supervised hierarchical classification framework identifies conserved features of E3 families and subfamilies, consistent with RING, HECT, and RBR classes. This classification explains functional segregation, identifies multi-subunit and standalone enzymes, and integrates substrate and small molecule interaction networks. Our analysis provides a global view of E3 biology, opening new strategies for drugging E3-substrate networks, including drug re-purposing and designing new E3 handles.
HostingRepository	PRIDE
AnnounceDate	2025-11-18
AnnouncementXML	Submission_2025-11-18_01:33:52.893.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thorsten Mosler
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-06 16:58:48	ID requested
⏵ 1	2025-11-18 01:33:53	announced

Dataset with its publication pending

submitter keyword: E3 ligase

Ramachandra M. Bhaskara
contact affiliation	Institute of Biochemistry II, Faculty of Medicine, Goethe University, Buchmann Institute for Molecular Life Sciences, Goethe University
contact email	Bhaskara@med.uni-frankfurt.de
lab head
Thorsten Mosler
contact affiliation	Goethe University Clinics Frankfurt
contact email	thorstenmosler@googlemail.com
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/2025/11/PXD067015

PRIDE project URI

• PRIDE
  1. PXD067015
     1. Label: PRIDE project
     2. Name: Multi-scale classification decodes the complexity of the human E3 ligome