PXD055923

PXD055923 is an original dataset announced via ProteomeXchange.

Title	Visualization of lysosomal membrane proteins by cryo-electron tomography
Description	Dysfunction in lysosomal membrane proteins and their associated complexes impairs the lysosome's essential role as a key signaling hub within the cell. This disruption underlies severe neurological disorders, such as lysosomal storage diseases and cancer. While direct visualization of the proteomic membrane environment of isolated lysosomes is crucial for advancing our understanding of its functions, it remains a significant challenge. To overcome this, we developed a method to enrich intact lysosomes using the essential lysosomal ion channel, transient receptor potential mucolipin 1. This enabled us to employ cryo electron tomography to reveal the heterogeneous molecular landscape of lysosomes. Notably, in concordance with quantitative mass spectrometry we identified protein densities on lysosomal membranes consistent with V-ATPase, Flotillin, clathrin-coated vesicles, mTORC1, HOPS, VPS13C, and dynein-dynactin. These findings demonstrate that our method offers a robust platform for advancing the structural and functional understanding of individual lysosomes, facilitating the visualization and resolution of endogenous protein complexes.
HostingRepository	PRIDE
AnnounceDate	2025-10-17
AnnouncementXML	Submission_2025-10-17_10:34:55.152.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD055923
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Marian Kalocsay
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-16 20:52:56	ID requested
⏵ 1	2025-10-17 10:34:55	announced

10.6019/PXD055923;

10.1038/S41467-025-64314-0;

submitter keyword: Lysosomes, lysosomal storage disorders, Cryo-electron tomografy, protein structures

Vera Moiseenkova-Bell
contact affiliation	Department of Physiology, Perelman School of Medicine, UPenn
contact email	vmb@pennmedicine.upenn.edu
lab head
Marian Kalocsay
contact affiliation	The University of Texas MD Anderson Cancer Center Department of Experimental Radiation Oncology
contact email	mkalocsay@mdanderson.org
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/PXD055923

PRIDE project URI

• PRIDE
  1. PXD055923
     1. Label: PRIDE project
     2. Name: Visualization of lysosomal membrane proteins by cryo-electron tomography