PXD068369

PXD068369 is an original dataset announced via ProteomeXchange.

Title	Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast
Description	Upf1 is a master regulator of nonsense-mediated mRNA decay (NMD), an mRNA surveillance and degradation pathway conserved from yeast to human. In S. cerevisiae, Upf1 exists in two distinct complexes with factors that mediate NMD activation or 5'-3' mRNA degradation. We combined endogenous purifications and biochemical reconstitutions of yeast Upf1 complexes with structural analyses and biochemical assays to elucidate the molecular mechanisms driving the mutually exclusive organization of the Upf1-5'-3' and Upf1-2-3 complexes. We show that yeast Upf1 is in a constitutive complex whereby its CH, RecA and C-terminal domains interact with the mRNA decapping factor Dcp2, NMD-associated proteins Nmd4 and Ebs1, and the 5' 3' exoribonuclease Xrn1, respectively. Together, the interacting surfaces and closed conformation of Upf1 in the Upf1-5'-3' complex sterically obstruct the binding of Upf2-3. Our work points to a major restructuring upon recruitment of these factors during NMD and provides insights into evolutionary divergence amongst species.
HostingRepository	PRIDE
AnnounceDate	2025-10-14
AnnouncementXML	Submission_2025-10-14_04:23:53.205.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Barbara Steigenberger
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-15 02:57:45	ID requested
⏵ 1	2025-10-14 04:23:54	announced

10.1016/j.celrep.2025.116415;

Iermak I, Wilson Eisele NR, Kurscheidt K, Loukeri MJ, Basquin J, Bonneau F, Langer LM, Keidel A, Conti E, Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast. Cell Rep, 44(10):116415(2025) [pubmed]

submitter keyword: Nonsense-mediated decay, cryo-EM, Saccharomyces cerevisiae, AlphaFold, biochemical reconstitution, Upf1, endogenous purification

Iuliia Iermak
contact affiliation	Paul Langerhans Institute Dresden and Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine TU Dresden, 01307 Dresden German Center for Diabetes Research 85764 Neuherberg, Germany
contact email	iermak@biochem.mpg.de
lab head
Barbara Steigenberger
contact affiliation	MPI of Biochemistry
contact email	steigenberger@biochem.mpg.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/2025/10/PXD068369

PRIDE project URI

• PRIDE
  1. PXD068369
     1. Label: PRIDE project
     2. Name: Molecular mechanisms governing the formation of distinct Upf1-containing complexes in yeast