⮝ Full datasets listing

PXD046995

PXD046995 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProtein binder based IP-MS of SLC12A6 (KCC3) in Hek293WT OE cell lines
DescriptionSpecific protein binders with high affinity, such as antibodies or nanobodies, are scarce for most solute carrier (SLCs) transporters. Moreover, general approaches that can systematically generate binders for multi-transmembrane proteins, such as SLCs, channels or GPCRs, are still missing. Purifying and reconstituting transmembrane proteins in their lipidic environments remain challenging, hence membrane proteins normally act as poor input material for binder generation. To overcome this challenge, we first identified state-of-the-art methods to generate protein binders targeting membrane transporters. Next, we produced full length protein or cell lines as input material for 27 SLCs, which were then processed in the selected binder generation platforms. As a result, we obtained >300 binders for 23 SLCs, 1 SLC failed and 3 SLCs are still in process. Then we established a cell-based validation workflow using immunofluorescent and immunoprecipitation methods to process all obtained binders. To further highlight the suitability of high-performance binders as an important tool for the biomolecular characterization of SLCs, we tested whether three SLC12A6 binders could be used in a quantitative co-immunoprecipitation followed by mass spectrometry (IP-MS) approach. This initial analysis of the IP-MS dataset showed that SLC12A6 specific binders are capable of strongly enriching SLC12A6. We also showed that despite high sequence similarity, the different binders showed different binder to target ratios, indicating different affinities to SLC12A6 in cell lysates. With this work, we were able to generate easily renewable and highly specific binders against SLCs, which will greatly facilitate the study of this neglected protein family.
HostingRepositoryPRIDE
AnnounceDate2024-06-17
AnnouncementXMLSubmission_2024-06-17_02:51:22.096.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFabian Frommelt
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-11-15 10:07:13ID requested
12024-06-17 02:51:22announced
Publication List
10.1016/J.JMB.2024.168665;
Keyword List
submitter keyword: Human, IP-MS, SLC12A6 (KCC3), protein binders
Contact List
Giulio Superti-Furga
contact affiliationCeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
contact emailgsuperti@cemm.oeaw.ac.at
lab head
Fabian Frommelt
contact affiliationCeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
contact emailfabian.frommelt@hotmail.com
dataset submitter
Full Dataset Link List
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/2024/06/PXD046995
PRIDE project URI
Repository Record List
[ + ]