<<< Full experiment listing

PXD023533

PXD023533 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleRab5a-VPS34 unnatural amino acid mediated crosslinking
DescriptionThe small GTPase Rab5 has an essential role in sorting vesicles arriving to and leaving the early endosome. One key function of Rab5 in this process is the activation of the primordial phosphatidylinositol 3-kinase VPS34, a lipid kinase that phosphorylates phosphatidylinositol (PI) to generate PI3P. Human VPS34 forms two heterotetrameric core complexes known as complexes I and II. Rab5a preferentially activates endocytic complex II in a membrane dependent manner. To map Rab5a-GTP interaction sites in complex II, unnatural amino acid mediated crosslinking was employed by genetic code expansion. A Rab5a mutant, in which the S84 in was replaced by BrCO6K was used for crosslinking mass spectrometry analysis. BrCO6K is a lysine derivative that can crosslink to several amino acids such as cysteines, histidines, lysines and glutamates over distances up to 15 Ã… (Cigler et al., 2017; Nguyen et al., 2018). Both complex II and VPS34 alone incubated with Rab5a-GTP-BrCO6K gave rise to a cross-linked product that ran slightly above the 120 kDa molecular weight marker, consistent with 102 kDa VPS34 crosslinked to the 24 kDa Rab5a (126 kDa). The gel bands of this crosslinking product in both samples were cut and analysed by LC-MS/MS for identification of crosslinks.
HostingRepositoryjPOST
AnnounceDate2021-12-21
AnnouncementXMLSubmission_2022-09-18_03:54:29.386.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD023533
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterZhuo Chen
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListS-carboxamidomethyl-L-cysteine; L-methionine sulfoxide
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-11 18:06:47ID requested
12021-12-21 07:18:43announced
22022-09-18 03:54:30announced2022-09-18: Updated FTP location.
Publication List
Tremel S, Ohashi Y, Morado DR, Bertram J, Perisic O, Brandt LTL, von Wrisberg MK, Chen ZA, Maslen SL, Kovtun O, Skehel M, Rappsilber J, Lang K, Munro S, Briggs JAG, Williams RL, Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Nat Commun, 12(1):1564(2021) [pubmed]
Keyword List
submitter keyword: Rab5a, VPS34, unnatural amino acid mediated crosslinking, crosslinking/mass spectrometry
Contact List
Juri Rappsilber
lab head
Zhuo Chen
contact affiliationTechnische Universität Berlin
dataset submitter
Full Dataset Link List
jPOST dataset URI
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.jpostdb.org/JPST001056/