PXD066163

PXD066163 is an original dataset announced via ProteomeXchange.

Title	Proximity proteomics on RPE1 stable cell lines with miniTurbo-p62 and ATG5 Knock-down to investigate p62 filaments and calcium-rich p62-enwrapped lipid droplets
Description	The selective autophagy receptor p62/SQSTM1 (from hereon p62) is known to form higher-order filaments in vitro and to undergo liquid-liquid phase separation when mixed with poly-ubiquitin. We determined the full-length cryo-EM structure of p62 and elucidated a structured double helical filament scaffold composed of the PB1-domain associated with the flexible C-terminal part residing in the lumen and the solvent-accessible major groove. At different pH values and upon binding to soluble LC3, LC3-conjugated membranes and poly-ubiquitin, we observed p62 filament re-arrangements in the form of structural unwinding, disassembly, lateral association and bundling, respectively. In the cellular environment, under conditions of ATG5 knockdown leading to stalled autophagy, we imaged high-contrast layers consisting of p62 oligomers enwrapping lipid droplets by cryogenic electron tomography in cellulo, which we identified as calcium as well as phosphorus by compositional spectroscopy analysis. Together, we visualized the cellular ultrastructure of p62 oligomers with high calcium content as a potential early stage of autophagy. Therefore, we performed proximity biotinylation and proteomics to identify calcium transporters and binding proteins in proximity to the p62 encapsulated lipid droplets.
HostingRepository	PRIDE
AnnounceDate	2025-12-08
AnnouncementXML	Submission_2025-12-07_16:26:08.512.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maya Marita Dierig
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	biotinylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-15 05:03:25	ID requested
⏵ 1	2025-12-07 16:26:09	announced

10.1038/s41467-025-66785-7;

Berkamp S, Jungbluth L, Katranidis A, Mostafavi S, Korculanin O, Lu PH, Ickert L, Dierig MM, Sharma L, Thukral L, Huesgen PF, Kononenko NL, Fitter J, Dunin-Borkowski RE, Sachse C, Structural organization of p62 filaments and the cellular ultrastructure of calcium-rich p62-enwrapped lipid droplet cargo. Nat Commun, 16(1):10810(2025) [pubmed]

submitter keyword: Human, LC-MS, Biotinylation, miniTurbo, ATG5 KD

Pitter Florian Huesgen
contact affiliation	University of Freiburg Faculty of Biology Biochemistry/Functional Proteomics Schänzlestr. 1 79104 Freiburg Germany
contact email	pitter.huesgen@biologie.uni-freiburg.de
lab head
Maya Marita Dierig
contact affiliation	MMD
contact email	maya.dierig@biologie.uni-freiburg.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/2025/12/PXD066163

PRIDE project URI

• PRIDE
  1. PXD066163
     1. Label: PRIDE project
     2. Name: Proximity proteomics on RPE1 stable cell lines with miniTurbo-p62 and ATG5 Knock-down to investigate p62 filaments and calcium-rich p62-enwrapped lipid droplets