PXD036885

PXD036885 is an original dataset announced via ProteomeXchange.

Title	De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography
Description	Understanding molecular mechanisms of cellular pathways regularly requires knowledge of the identities of participating proteins, their cellular localization and their 3D structures. Contemporary workflows typically require multiple techniques to identify target proteins, track their localization using fluorescence microscopy, followed by in vitro structure determination. To identify mammal-specific sperm proteins and understand their functions, we developed a visual proteomics workflow to directly address these challenges. Our in situ cryo-electron tomography analyses of mouse and human sperm revealed key microtubule structures at 6.0 Å resolution via subtomogram averaging. The well-resolved secondary and tertiary structures allowed us to unbiasedly match novel densities discovered in our 3D reconstruction maps with 21615 protein models from the library of the mouse proteome generated by AlphaFold2. Additional biochemical and mass spectrometry analyses helped validate potential candidates. Not only was it possible to de novo identify novel mammal-specific sperm proteins using this label-free structural approach, but their cellular localizations and molecular interactions could be determined in situ. Specifically, the novel sperm proteins form an extensive interaction network crosslinking the lumen of microtubules, suggesting they could modulate the mechanical and elastic properties of the microtubule filaments required for the vigorous beating motions of flagella. This project includes global protein abundance data from five biochemical fractionations of mouse sperm cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:40:09.948.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Robyn Kaake
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-21 01:06:09	ID requested
1	2024-05-21 09:23:19	announced
⏵ 2	2024-10-22 06:40:14	announced	2024-10-22: Updated project metadata.

Chen Z, Shiozaki M, Haas KM, Skinner WM, Zhao S, Guo C, Polacco BJ, Yu Z, Krogan NJ, Lishko PV, Kaake RM, Vale RD, Agard DA, De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking. Cell, 186(23):5041-5053.e19(2023) [pubmed]

10.1016/j.cell.2023.09.017;

submitter keyword: Global protein abundance, in situ cryoET, mouse sperm axoneme, sperm flagella, visual proteomics

Robyn Kaake
contact affiliation	Dept. Cellular Molecular Pharmacology, University of California - San Francisco (UCSF), USA
contact email	robyn.kaake@gladstone.ucsf.edu
lab head
Robyn Kaake
contact affiliation	Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
contact email	robyn.kaake@gladstone.ucsf.edu
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/2024/05/PXD036885

PRIDE project URI

• PRIDE
  1. PXD036885
     1. Label: PRIDE project
     2. Name: De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography