PXD061277

PXD061277 is an original dataset announced via ProteomeXchange.

Title	A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution
Description	RAB5-GTP activation of the multiprotein VPS34 complex II (VPS34-CII) is critical for endosomal sorting and maturation, phagocytosis, and receptor downregulation. RAB5-GTP activates VPS34-CII, by binding to a helical insertion in the C2 domain of VPS34 on the BECLIN1/UVRAG-containing adaptor arm of the complex. The autophagy complex, VPS34 complex I (VPS34-CI), features a unique ATG14L subunit in place of the VPS34-CII UVRAG subunit, and we found that this distorts the adaptor arm to alter the VPS34 RAB-GTPase binding pocket so that it preferentially binds RAB1-GTP. Surprisingly, our higher-resolution single-particle cryo-EM structure of VPS34-CII showed a second RAB5-GTP binding site on the VPS15 solenoid region. This site (VPS15-RAB5-site) appears to be the primordial RAB5-binding region. A mutant in the helical insertion of the C2 domain of human VPS34 that mimics the Saccharomyces cerevisiae sequence abolishes RAB5 binding to VPS34. Mutation of the VPS15-RAB5-site ortholog in S. cerevisiae VPS15 resulted in defective CPY sorting, loss of colocalizsation with the RAB5 ortholog Vps21, and loss of binding to Vps21 in vitro. Evolutionary expansion from one to two RAB5-orthologue binding sites may have increased membrane binding and VPS34-CII activity to adapt to more complex endocytic systems.
HostingRepository	PRIDE
AnnounceDate	2026-05-26
AnnouncementXML	Submission_2026-05-26_09:22:30.268.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maxime Bourguet
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-02-27 10:00:41	ID requested
⏵ 1	2026-05-26 09:22:30	announced

10.7554/ELIFE.110040.3;

submitter keyword: None

Roger Lee
contact affiliation	MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
contact email	rlw@mrc-lmb.cam.ac.uk
lab head
Maxime Bourguet
contact affiliation	MRC Laboratory of Molecular Biology
contact email	mbourguet@mrc-lmb.cam.ac.uk
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/2026/05/PXD061277

PRIDE project URI

• PRIDE
  1. PXD061277
     1. Label: PRIDE project
     2. Name: A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution