PXD046991

PXD046991 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS analysis of ribosome UFMylation in vitro
Description	UFMylation, is a Ubiquitin-like modification occurring on RPL26, a ribosomal subunit, upon ribosome stalling at the ER membrane. This modification is achieved by a pool of enzymes commonly referred to as E1-activating, E2-conjugating and E3-ligase enzymes. The UFM1 E3 ligase comprises of three proteins: UFL1, UFBP1 and CDK5RAP3, referred to as UFM1 Ribosome E3 Ligase (UREL) complex. While UFL1 and UFBP1 are sufficient for E3 ligase activity in vitro, CDK5RAP3 is indispensable for ribosome UFMylation in vivo. In this work, we characterize in vitro UFMylation reaction of purified 60S ribosomes in the presence and absence of CDK5RAP3 using LC-MS/MS. Specifically, we analyse sites of UFMylation, linkage type and quantify monoUFMylation and diUFMylation on RPL26. Interestingly, we find UFMylation to occur on a specific lysine residue, K134, in the presence of UFL1/UFBP1 alone and in complex with CDK5RAP3. In addition, we also provide quantitative information on relative abundances of RPL26 mono- and di-UFMylation under these conditions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:34:23.978.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Frederic Lamoliatte
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 240

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-15 08:12:09	ID requested
1	2024-03-22 01:42:49	announced
⏵ 2	2024-10-22 06:34:25	announced	2024-10-22: Updated project metadata.

10.1038/s41586-024-07093-w;

Makhlouf L, Peter JJ, Magnussen HM, Thakur R, Millrine D, Minshull TC, Harrison G, Varghese J, Lamoliatte F, Foglizzo M, Macartney T, Calabrese AN, Zeqiraj E, Kulathu Y, The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Nature, 627(8003):437-444(2024) [pubmed]

submitter keyword: In vitro reconstitution, RPL26 UFMylation , Ribosome UFMylation

Yogesh Kulathu
contact affiliation	Medical Research Council Protein Phosphorylation and Ubiquitylation Unit School of Life Sciences, University of Dundee, Dundee, Scotland
contact email	y.kulathu@dundee.ac.uk
lab head
Frederic Lamoliatte
contact affiliation	University of Dundee
contact email	flamoliatte001@dundee.ac.uk
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/2024/03/PXD046991

PRIDE project URI

• PRIDE
  1. PXD046991
     1. Label: PRIDE project
     2. Name: LC-MS/MS analysis of ribosome UFMylation in vitro