PXD031962

PXD031962 is an original dataset announced via ProteomeXchange.

Title	Hydrogen-deuterium exchange mass spectrometry of wt Mtr4 with various RNA substrates
Description	Mtr4 is a eukaryotic RNA helicase required for RNA decay by the nuclear exosome. Previous studies have shown how RNA enroute to the exosome threads through the highly conserved helicase core of Mtr4. Mtr4 also contains an arch domain, although details of potential interactions between the arch and RNA have been elusive. To understand the interaction of Saccharomyces cerevisiae Mtr4 with various RNAs, we have characterized RNA binding in solution using hydrogen-deuterium exchange mass spectrometry, and affinity and unwinding assays. We have identified RNA interactions within the helicase core that are consistent with existing structures and do not vary between tRNA, single-stranded RNA, and double-stranded RNA constructs. We have also identified novel RNA interactions with a region of the arch known as the fist or KOW. These interactions are important for RNA unwinding and vary in strength depending on RNA structure and length. They account for Mtr4 discrimination between different RNAs. These interactions further drive Mtr4 to adopt a closed conformation characterized by reduced dynamics of the arch arm and intra-domain contacts between the fist and helicase core.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:35:19.555.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sheena D'Arcy
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-01 09:59:03	ID requested
1	2022-03-07 12:57:57	announced
⏵ 2	2024-10-22 05:35:19	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

ProteomeXchange project tag: Hydrogen Deuterium Exchange (HDX-MS)

submitter keyword: HDX, helicase, HDX-MS,Mtr4, bottom-up HDX

Sheena D'Arcy
contact affiliation	Department of Chemistry and Biochemistry, The University of Texas at Dallas, Dallas, TX, 75013, USA
contact email	sheena.darcy@utdallas.edu
lab head
Sheena D'Arcy
contact affiliation	The University of Texas at Dallas
contact email	sheena.darcy@utdallas.edu
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/2022/03/PXD031962

PRIDE project URI

• PRIDE
  1. PXD031962
     1. Label: PRIDE project
     2. Name: Hydrogen-deuterium exchange mass spectrometry of wt Mtr4 with various RNA substrates