PXD003736

PXD003736 is an original dataset announced via ProteomeXchange.

Title	Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomal particles
Description	Ribosome biogenesis is a highly complex process in eukaryotes, involving temporally and spatially regulated ribosomal protein (r-protein) binding and rRNA remodeling events in the nucleolus, nucleoplasm and cytoplasm. Hundreds of assembly factors (AFs), organized into sequential functional groups, facilitate and guide the maturation process into productive assembly branches in and across different cellular compartments. However, the precise mechanisms by which these AFs function are largely unknown. Here, we use cryo-electron microscopy (cryo-EM), to characterize the structures of yeast nucleoplasmic pre-60S particles affinity-purified using the epitope-tagged AF Nog2. Our data pinpoint the locations and determine the structures of over 20 AFs, which are enriched in two areas, an arc region extending from the central protuberance (CP) to the polypeptide tunnel exit (PTE), and the domain including the internal transcribed spacer 2 (ITS2) that separates 5.8S and 25S rRNAs. These structural data suggest that the arc-located factors might function to chaperone formation of RNA helices found in the active sites of the subunit, including helices from the CP, peptidyl-transferase center (PTC) and intersubunit bridge. In particular, two regulatory GTPases, Nog2 and Nog1, act as hub proteins to interact with multiple, distant AFs and functional rRNA elements, manifesting their critical roles in structural remodeling checkpoints and nuclear export. Moreover, our snapshots of compositionally and structurally different pre-60S intermediates provide essential mechanistic details for three major remodeling events before nuclear export: rotation of the 5S RNP, construction of the active center, and ITS2 removal. Therefore, our structures provide a framework to understand the molecular roles of diverse AFs, and potentially the atomic information therein constitutes a resource to generalize principles governing the elusive functions of nuclear RNA-binding proteins.
HostingRepository	PRIDE
AnnounceDate	2016-06-01
AnnouncementXML	Submission_2016-06-06_04:44:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luyao Ma
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-03-03 02:26:15	ID requested
1	2016-06-01 01:57:25	announced
⏵ 2	2016-06-06 04:44:51	announced	Updated publication reference for PubMed record(s): 27251291.

Wu S, Tutuncuoglu B, Yan K, Brown H, Zhang Y, Tan D, Gamalinda M, Yuan Y, Li Z, Jakovljevic J, Ma C, Lei J, Dong MQ, Woolford JL, Gao N, Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Nature, 534(7605):133-7(2016) [pubmed]

curator keyword: Biological

submitter keyword: Pre-60S ribosome, assembly factors, cryo-EM, CXMS

Meng-Qiu Dong
contact affiliation	National Institute of Biological Sciences, Beijing, Beijing, China.
contact email	dongmengqiu@nibs.ac.cn
lab head
Luyao Ma
contact affiliation	National Institute of Biological Sciences, Beijing.
contact email	maluyao@nibs.ac.cn
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/2016/06/PXD003736

PRIDE project URI

• PRIDE
  1. PXD003736
     1. Label: PRIDE project
     2. Name: Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomal particles