PXD054983-1

PXD054983 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Proteasomal Compositional and Conformational Landscapes Mapped By in-situ Cross-Linking Mass Spectrometry
Description	The proteasome is a vital cellular machine responsible for degrading proteins and maintaining proteostasis. While cryo-EM and cross-linking mass spectrometry (XL-MS) have provided valuable structural insights, these investigations have primarily focused on purified proteasomes in vitro. Here, we perform XL-MS in-situ with an enrichable trifunctional cross-linker to characterize the proteasome within its native cellular environment. Leveraging a two-step enrichment strategy and the high effective protein concentrations within cellular compartments, we generated a comprehensive dataset of proteasome-centered cross-links, which unveiled novel interacting proteins and enabled the construction of dynamic structural models of the proteasome. Furthermore, by resolving nuclear and cytoplasmic fractions, we uncovered distinct proteasome compositions, structural dynamics, and interaction profiles in these two compartments. The cross-linking data also informed AI-based structural predictions and provided crucial restraints for refining docking models. Our integrated approach establishes a powerful workflow for investigating the architecture, functional dynamics, and regulation of large protein complexes in situ, offering deeper insights of their regulatory mechanisms and cellular functions.
HostingRepository	jPOST
AnnounceDate	2025-08-18
AnnouncementXML	Submission_2025-08-17_08:00:05.299.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lili Zhao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	LTQ Orbitrap

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-19 04:24:04	ID requested
⏵ 1	2025-08-17 08:00:05	announced

Publication List

Dataset with its publication pending

Dataset with its publication pending

Keyword List

submitter keyword: LC-MS/MS, chemical cross-lining, proteasome

submitter keyword: LC-MS/MS, chemical cross-lining, proteasome

Contact List

Lihua Zhang
lab head
Lili Zhao
contact affiliation	DICP
dataset submitter

Full Dataset Link List

jPOST dataset URI
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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/JPST003290/