PXD029930

PXD029930 is an original dataset announced via ProteomeXchange.

Title	Sensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry
Description	The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling, but little is known about the structural characteristics of UV-induced cross-links. Here we demonstrate protocol optimizations, and apply the enhanced protocol to a set of model protein-RNA complexes to better characterize the properties of UV-induced protein-RNA cross-links. We use these insights to study a non-canonical protein-RNA interaction between SF3A1 of the U2 snRNP and stem-loop 4 of the U1 snRNP, demonstrating that UV cross-linking and mass spectrometry is a reliable standalone data type for low resolution structural characterizations of protein-RNA interactions.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:49:30.997.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Sarnowski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-26 02:02:50	ID requested
1	2023-09-06 01:33:52	announced
⏵ 2	2023-11-14 07:49:31	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: UV cross-linking

MBNL1

FOX1

PTBP1

SF3A1

U1

U2

cross-linking

XL-MS

structural proteomics

protein-RNA

RNA-protein

protein-RNA complex

RNA-protein complex

CLIR-MS

Alexander Leitner
contact affiliation	ETH Zurich, Institute of Molecular Systems Biology
contact email	leitner@imsb.biol.ethz.ch
lab head
Christopher Sarnowski
contact affiliation	Institute of Molecular Systems Biology, Department of Biology, ETH Zürich
contact email	sarnowski@imsb.biol.ethz.ch
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/2023/09/PXD029930

PRIDE project URI

• PRIDE
  1. PXD029930
     1. Label: PRIDE project
     2. Name: Sensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry