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PXD035828 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSpatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells
DescriptionThe protein structures and interactions that maintain and regulate cellular processes in different subcellular organelles are heterogeneous and dynamic. However, it remains challenging to characterize the subcellular specificity and translocation of protein complexes in terms of conformation and interactions. Herein, we developed a spatially resolved protein complex profiling approach by biocompatible chemical cross-linking in living cells (SPACX) to monitor the dynamics of protein conformation, interactions and translocation. The advancement of fast capturing protein complexes in the physiological state, coupled with efficient enrichment of the cross-linked peptides, ensured deep-coverage analysis of the protein interactome in living cells. By ensemble structure refinement with cross-linking restraints, subcellular-specific conformation heterogeneity was identified for PTEN. PTEN displayed a broader range of dynamic conformation changes on the dual specificity domains in the nucleus than in the cytoplasm. Moreover, based on conformational differences, different interacting assemblies involving 25 cytoplasm-exclusively and 18 nucleus-exclusively PTEN-interacting proteins were found to account for diverse biological functions. Upon ubiquitin-proteasome system (UPS) stress, the assembly of PTEN and its interacting partners changed obviously during translocation. We newly identified 36 PTEN-interacting proteins, which were found to be highly enriched in functional pathways closely related to cell apoptosis. Inspiringly, the interactions among PTEN isoforms and their interacting proteins were accessible by the determination of sequence-unique cross-linking interfaces for direct interactions. All these results indicate the promise of SPACX to elucidate the functional heterogeneity of proteins in individual subcellular sociology.
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterrong Bei Zhang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListS-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-08-05 04:16:48ID requested
12022-08-05 04:28:16announced
22022-09-18 03:37:48announced2022-09-18: Updated FTP location.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: in vivo cross-linking, protein-protein interaction, protein conformation
Contact List
Lihua Zhang
lab head
rong Bei Zhang
contact affiliationDalian Institute of Chemical Physics, Chinese Academy of Sciences
dataset submitter
Full Dataset Link List
jPOST dataset URI
Dataset FTP location
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