PXD056163-1

PXD056163 is an original dataset announced via ProteomeXchange.

Title	The structure and function of P5A-ATPases
Description	In eukaryotes P5A-ATPases are resident in the endoplasmic reticulum (ER) membrane. Their dysfunction causes broad and unspecific phenotypes, with effects on protein biogenesis and quality control. While P5A-ATPases have been suggested to remove misinserted proteins from the membrane, the molecular function remains debated. Here, we report cryo-EM structures reaching 3.2 Å overall resolution of a eukaryotic P5A-ATPase member, CtSpf1, covering multiple transport intermediates of the E1→E1-ATP→E1P-ADP→E1P→E2P→E2.Pi→E2 cycle. In the E2P and E2.Pi states a cleft spans the entire membrane, holding a polypeptide cargo molecule. The cargo includes an ER luminal extension, pinpointed as the C-terminus in the E2.Pi state, which reenters the membrane in E2P. The E1 structure harbors a cytosol-facing cavity that is blocked by an insertion into the central P-domain, here referred to as the Plug-domain. The Plug-domain is nestled to key ATPase features and is displaced in the E1P-ADP and E1P states. Interestingly, a complementary cryo-EM feature is detected also in the E1P-ADP conformation, located peripherally to the above-mentioned cargo. Collectively, our structural and mass spectrometry data are compatible with a broad range of proteins as cargo, with the P5A-ATPases serving a role in membrane removal, although membrane insertion/secretion cannot be excluded. Our work also reveals a critical mechanistic role of the Plug-domain and certain N-terminal transmembrane segments, where the latter couple conformational changes to structural changes of the soluble domains.
HostingRepository	PRIDE
AnnounceDate	2024-11-08
AnnouncementXML	Submission_2024-11-08_05:07:34.954.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Per Hägglund
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-24 03:03:10	ID requested
⏵ 1	2024-11-08 05:07:35	announced

10.1038/S41467-024-53757-6;

submitter keyword: cryo-EM,ATPase, membrane protein, LC-MS/MS

Per Hägglund
contact affiliation	Department of Biomedical Sciences, Copenhagen University, Nørre Allé 14, DK-2200 Copenhagen N, Denmark
contact email	hagglundperm@gmail.com
lab head
Per Hägglund
contact affiliation	University of Copenhagen
contact email	hagglundperm@gmail.com
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/2024/11/PXD056163

PRIDE project URI

• PRIDE
  1. PXD056163
     1. Label: PRIDE project
     2. Name: The structure and function of P5A-ATPases