PXD058994-1

PXD058994 is an original dataset announced via ProteomeXchange.

Title	A comprehensive view on r- protein binding and rRNA domain structuring during early ribosome formation
Description	Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) while removing internal (ITS) and external (ETS) transcribed rRNA spacers. During early stages of large subunit (LSU) formation, ITS2 together with six assembly factors forms the characteristic foot structure of early nuclear pre-LSU particles. Here, we address the function of this foot structure during early stages of ribosome assembly. We present cryo-EM structures from wild-type cells and cells depleted for the foot structure factor Rlp7. We show that compaction of domain I of the 25S rRNA is strictly dependent on the presence of foot factors, while domain II folds independently. Furthermore, Rlp7-depletion accumulated small subunit (SSU) processome intermediates prior A1 cleavage and compaction of the individual domains of the 18S rRNA, providing also novel insights into the SSU-assembly process. SILAC labeling and affinity purification of co-transcriptional assembled pre-ribosomes enabled us to resolve the assembly line of the r-proteins step by step. This showed that incorporation of r-proteins in eukaryotes neither follows the bacterial regime nor a strict linear co-transcriptional mode. Instead, seed r-proteins might structurally define the individual rRNA domains before their compaction and fixation in the context of the SSU processome.
HostingRepository	PRIDE
AnnounceDate	2026-02-02
AnnouncementXML	Submission_2026-02-01_16:27:02.942.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juliane Merl-Pham
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-18 07:44:50	ID requested
⏵ 1	2026-02-01 16:27:04	announced

Gerhalter M, Prattes M, Grundmann LE, Grishkovskaya I, Semeraro EF, Zisser G, Kotisch H, Merl-Pham J, Hauck SM, Haselbach D, Bergler H, A comprehensive view on r-protein binding and rRNA domain structuring during early eukaryotic ribosome formation. Nucleic Acids Res, 54(3):(2026) [pubmed]

10.1093/nar/gkag036;

submitter keyword: Ribosome biogenesis, single particle cryo-EM, LSU assembly, SSU processome, rRNA domain folding, ribosomal protein assembly

Helmut Bergler
contact affiliation	Institute of Molecular Biosciences, University of Graz, Graz, 8010, Austria
contact email	helmut.bergler@uni-graz.at
lab head
Juliane Merl-Pham
contact affiliation	Metabolomics and Proteomics Core, Helmholtz Munich
contact email	juliane.merl@helmholtz-muenchen.de
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/2026/02/PXD058994

PRIDE project URI

• PRIDE
  1. PXD058994
     1. Label: PRIDE project
     2. Name: A comprehensive view on r- protein binding and rRNA domain structuring during early ribosome formation