PXD009224

PXD009224 is an original dataset announced via ProteomeXchange.

Title	Chemical cross-linking enables drafting ClpXP proximity maps and taking snapshots of in vivo interaction networks
Description	Protein-protein interactions within complexes and networks are often dynamic and their elucidation remains a challenging task. Here, we show on the example of the proteolytic ClpXP complex the power of combined chemical cross-linking and mass-spectrometry to capture transient binding interactions within ClpP and ClpX as well as across the enigmatic ClpX hexamer – ClpP heptamer interface. Our data suggests that a few hot spot lysine residues located in signature loops in ClpX mediate the ClpX-ClpP interaction. This study further confirms that Listeria monocytogenes ClpX solely interacts with the heterooligomeric ClpP1/2 complex via the ClpP2 apical site. Moreover, the cellular interaction network of human and bacterial proteases was elucidated via in situ chemical cross-linking followed by an antibody-based pull-down against ClpP from genetically unmodified cells. A subsequent gel-free, quantitative mass spectrometric analysis demonstrated an up to 3-fold higher coverage compared to conventional co-immunoprecipitation without cross-linker revealing unprecedented insight into intracellular ClpXP networks.
HostingRepository	PRIDE
AnnounceDate	2018-11-21
AnnouncementXML	Submission_2018-11-21_04:56:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anja Fux
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Staphylococcus aureus; NCBI TaxID: 1280;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion ETD; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-03-15 08:07:50	ID requested
⏵ 1	2018-11-21 04:56:01	announced

Fux A, Korotkov VS, Schneider M, Antes I, Sieber SA, Chemical Cross-Linking Enables Drafting ClpXP Proximity Maps and Taking Snapshots of In Situ Interaction Networks. Cell Chem Biol, 26(1):48-59.e7(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: chemical cross-linking, ClpP, ClpXP, co-IP, interacting proteins

Stephan A. Sieber
contact affiliation	Technical University Munich Department of Chemistry Chair for organic Chemistry II Lichtenbergstraße 4 Garching bei München D-85748 Germany
contact email	stephan.sieber@tum.de
lab head
Anja Fux
contact affiliation	Techincal University Munich
contact email	anja.fux@tum.de
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/2018/11/PXD009224

PRIDE project URI

• PRIDE
  1. PXD009224
     1. Label: PRIDE project
     2. Name: Chemical cross-linking enables drafting ClpXP proximity maps and taking snapshots of in vivo interaction networks