PXD064127-1

PXD064127 is an original dataset announced via ProteomeXchange.

Title	Anti-sense oligonucleotide inhibited iSAT reaction
Description	Investigating the intricate and rapid folding kinetics of large RNA-protein complexes (RNPs), like the bacterial ribosome, remains a formidable challenge in structural biology. Previous genetic approaches to probe assembly have focused on modulating the expression of either r-proteins or assembly factors. Here, anti-sense oligonucleotides (ASOs) were used to disrupt native RNA/RNA and RNA/protein interactions, in order to generate previously uncharacterized folding intermediates. In an in vitro co-transcriptional ribosome assembly assay, 10 assembly inhibitor ASOs were identified. Using cryo-electron microscopy, 38 intermediate structures were determined resulting from the specific inhibitions generated by 6 inhibitory ASOs. A notable intermediate class provided compelling evidence for independent rRNA domain folding before proper interdomain docking. Three PNAs targeting domain-I of 23S rRNA further subdivided the previously identified assembly core into smaller blocks representing the earliest steps in assembly. The resulting assembly graph reveals template-directed RNA docking of defined regions as foldons, and domain consolidation, which provides a hierarchical view of the RNP assembly process. This approach not only identified potential targets for antibiotic development but also established a platform for probing the structure and dynamics of RNP assemblies.
HostingRepository	PRIDE
AnnounceDate	2025-07-28
AnnouncementXML	Submission_2025-07-27_16:23:00.276.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kai Sheng
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-20 16:39:01	ID requested
⏵ 1	2025-07-27 16:23:01	announced

10.1038/s41467-025-61640-1;

Sheng K, Dong X, Aiyer S, Lee J, Đ, or, đ, evi, ć, -Marquardt S, Lyumkis D, Williamson JR, Anti-sense oligonucleotide probing as a structural platform for studying ribonucleoprotein complex assembly. Nat Commun, 16(1):6642(2025) [pubmed]

submitter keyword: sucrose gradient fractions, iSAT,ribosome biogenesis

James Williamson
contact affiliation	Department of Integrative Structural and Computational Biology, Scripps Research Institute
contact email	jrwill@scripps.edu
lab head
Kai Sheng
contact affiliation	Scripps Research Institute
contact email	ksheng@scripps.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/2025/07/PXD064127

PRIDE project URI

• PRIDE
  1. PXD064127
     1. Label: PRIDE project
     2. Name: Anti-sense oligonucleotide inhibited iSAT reaction