PXD025992

PXD025992 is an original dataset announced via ProteomeXchange.

Title	E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP
Description	RNF213 is a giant E3 ubiquitin ligase and a major susceptibility factor of Moyamoya disease, a cerebrovascular disorder that can result in stroke or death. In the cell, RNF213 is involved in lipid droplet formation, lipotoxicity, hypoxia, and NF-κB signaling, but its exact function in these processes is unclear. Structural characterization has revealed the presence of a dynein-like ATPase module and an unprecedented but poorly understood E3 module. Here, we demonstrate that RNF213 E3 activity is dependent on ATP binding, rather than ATP hydrolysis, and is particularly responsive to the ATP/ADP/AMP ratio. Biochemical and activity-based probe analyses identify a non-canonical zinc finger domain as the E3 active site, which utilizes the strictly conserved Cys4462, not involved in zinc coordination, as the reactive nucleophile. The cryo-EM structure of the trapped RNF213:E2~Ub intermediate reveals RNF213 C-terminal domain as the E2 docking site, which positions the ubiquitin-loaded E2 proximal to the catalytic zinc finger, facilitating nucleophilic attack of Cys4462 on the E2~Ub thioester. Our findings show that RNF213 represents an undescribed type of a transthiolation E3 enzyme and is regulated by adenine nucleotide concentration via its ATPase core, possibly allowing it to react to changing metabolic conditions in the cell. XL-MS is used to identify the acceptor nucleophile that takes over the Ubiquitin moiety from ubiquitin-loaded UBE2L3, using a specially designed activity-based probe.
HostingRepository	PRIDE
AnnounceDate	2026-08-18
AnnouncementXML	Submission_2026-08-18_06:48:28.211.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juraj Ahel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-13 03:29:53	ID requested
⏵ 1	2026-08-18 06:48:29	announced

10.1038/s41467-025-59444-4;

Ahel J, Balci A, Faas V, Grabarczyk DB, Harmo R, Squair DR, Zhang J, Roitinger E, Lamoliatte F, Mathur S, Deszcz L, Bell LE, Lehner A, Williams TL, Sowar H, Meinhart A, Wood NT, Clausen T, Virdee S, Fletcher AJ, ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213. Nat Commun, 16(1):4414(2025) [pubmed]

submitter keyword: RNF213;UBE2L3;ABP

Tim Clausen
contact affiliation	Institute of Molecular Pathology (IMP), Vienna BioCenter, Vienna, Austria
contact email	tim.clausen@imp.ac.at
lab head
Juraj Ahel
contact affiliation	IMP Vienna
contact email	juraj.ahel@imp.ac.at
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/2026/08/PXD025992

PRIDE project URI

• PRIDE
  1. PXD025992
     1. Label: PRIDE project
     2. Name: E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP