PXD063485

PXD063485 is an original dataset announced via ProteomeXchange.

Title	Identifying insect cell proteins copurified with wild-type human UBR4/KCMF1/CALM1 complex and different domain deletions
Description	The UBR4/KCMF1/CALM1 complex is an important general protein quality control enzyme which extends ubiquitin chains on pre-ubiquitinated proteins to target them for degradation. We observed by cryogenic electron microscopy that the complex purified recombinantly from insect cells is bound to a potential substrate which cannot be identified by experimental density. However, we could determine that the copurified protein is bound to a certain domain in the complex termed the ZZ-DZB domain. To identify the copurified insect cell proteins we performed LC-MS analysis of the purified wild-type complex and a complex with the ZZ-DZB domain deleted. We compared the two datasets to identify proteins which were highly enriched in the wildtype dataset but lost in the ZZ-DZB deletion dataset. To gain additional insight into the role of the domains of UBR4 in substrate recognition, we repeated this approach with two other domain deletions – the BS2 domain and the UBL domain. As the UBR4/KCMF1/CALM1 complex is expected to recognize proteins by the processing of their N-termini, we also performed digests with three different proteases to try and identify the native N-termini of the co-purified proteins.
HostingRepository	PRIDE
AnnounceDate	2025-09-02
AnnouncementXML	Submission_2025-09-02_05:44:45.096.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Imre
SpeciesList	scientific name: Trichoplusia ni; NCBI TaxID: 7111;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-30 02:29:33	ID requested
⏵ 1	2025-09-02 05:44:45	announced

10.1126/SCIENCE.ADV9309;

submitter keyword: UBR4,Ubiquitin E3 ligase, KCMF1, trichoplusia ni, high-five insect cell expression

Tim Clausen
contact affiliation	Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
contact email	tim.clausen@imp.ac.at
lab head
Richard Imre
contact affiliation	IMBA Vienna
contact email	richard.imre@imba.oeaw.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063485
     1. Label: PRIDE project
     2. Name: Identifying insect cell proteins copurified with wild-type human UBR4/KCMF1/CALM1 complex and different domain deletions