PXD064958-1

PXD064958 is an original dataset announced via ProteomeXchange.

Title	Structure of an Archaeal Ribosome Reveals a Divergent Active Site and Hibernation Factor
Description	Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase center (PTC), is thought to be nearly universally conserved. Here, we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify a previously undescribed archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome
HostingRepository	PRIDE
AnnounceDate	2025-06-17
AnnouncementXML	Submission_2025-06-17_09:24:27.997.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD064958
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Robert Maxwell
SpeciesList	scientific name: Pyrobaculum calidifontis; NCBI TaxID: 181486;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-12 14:13:40	ID requested
⏵ 1	2025-06-17 09:24:28	announced

10.6019/PXD064958;

submitter keyword: LC-MS/MS, Ribosome, pyrobaculum calidifontis

Jamie H. D. Cate
contact affiliation	Innovative Genomics Institute, Room 212C 2151 Berkeley Way Berkeley CA 94720
contact email	j-h-doudna-cate@berkeley.edu
lab head
Robert Maxwell
contact affiliation	UCB
contact email	Robmaxwell@berkeley.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/2025/06/PXD064958

PRIDE project URI

• PRIDE
  1. PXD064958
     1. Label: PRIDE project
     2. Name: Structure of an Archaeal Ribosome Reveals a Divergent Active Site and Hibernation Factor