PXD056680

PXD056680 is an original dataset announced via ProteomeXchange.

Title	The structural scaffold of the TPLATE complex deforms the membrane during plant endocytosis
Description	Eukaryotic cells maintain homeostasis of their outer membrane by controlled internalization of lipid and protein constituents by endocytosis (Kaksonen & Roux, Nat Rev Mol Cell Biol. 2018). Endocytosis is evolutionary conserved and utilizes similar structural folds. How these structural folds are combined into proteins and protein complexes however differs between eukaryotic kingdoms (Kraus, Pleskot & Van Damme, Ann review 2024). The TPLATE complex in plants is an evolutionary ancient protein module that combines several endocytic folds into a single octameric protein complex (Gadeyne et al., Cell 2014, Hirst et al., eLife 2014, More et al., Curr Biol. 2020). Its molecular architecture, lipid-nucleated condensate formation, and its requirement for clathrin cage curvature revealed its function in endocytosis initiation in plants (Yperman & Wang et al., Sci Adv. 2021, Dragwidge et al., Nat Cell Biol. 2024, Johnson et al., PNAS 2021). Mechanistic understanding of how this complex drives membrane deformation during plant endocytosis is, however, lacking. Here, we used an integrative structural approach to obtain a precise molecular structure of the TPLATE complex. In addition, our approach also allowed visualizing the structural flexibility that hallmarks this enigmatic complex. We prove that the intrinsic structural flexibility is required for its functionality and membrane recruitment. We map different lipid-binding preferences onto specific domains located at the curved face of the complex. Finally, we show that the crescent shape of the structured part of the complex is sufficient for membrane curvature generation. Our mechanistic insight answers the longstanding question of how plants can execute endocytosis without cytoskeletal-based force generation.
HostingRepository	PRIDE
AnnounceDate	2025-11-06
AnnouncementXML	Submission_2025-11-06_12:00:34.776.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dominique Eeckhout
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: NEWT:3702;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-10 01:43:02	ID requested
⏵ 1	2025-11-06 12:00:35	announced

10.1038/S41477-025-02146-Y;

submitter keyword: AP-MS,Arabidopsis, structure, TPLATE complex, endocytosis, crosslinking-MS

Daniel Van Damme
contact affiliation	Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
contact email	daniel.vandamme@psb.vib-ugent.be
lab head
Dominique Eeckhout
contact affiliation	Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
contact email	dominique.eeckhout@psb.ugent.be
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/2025/11/PXD056680

PRIDE project URI

• PRIDE
  1. PXD056680
     1. Label: PRIDE project
     2. Name: The structural scaffold of the TPLATE complex deforms the membrane during plant endocytosis