PXD019771

PXD019771 is an original dataset announced via ProteomeXchange.

Title	The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains
Description	The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase that generates linear/Met1-linked ubiquitin chains. One of the LUBAC components, HOIL-1L, was recently shown to catalyse oxyester bond formation between the C-terminus of ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. We present the first 3D reconstruction of LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that addition of the oxyester-bound branches depends on HOIL-1L catalytic activity. We suggest a coordinated ubiquitin relay mechanism between the HOIP and HOIL-1L ligases supported by cross-linking mass spectrometry data, which show proximity between the catalytic RBR domains. Mutations in the linear ubiquitin chain-binding NZF domain of HOIL-1L reduces chain branching confirming its role in the process. In cells, these heterotypic chains were induced by TNF. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains with linear and oxyester-linked branches by the concerted action of HOIP and HOIL-1L.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:23:23.149.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019771
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Antonia Vogel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-15 02:49:50	ID requested
1	2021-06-28 02:11:47	announced
2	2021-06-28 06:46:14	announced	2021-06-28: Updated project metadata.
⏵ 3	2024-10-22 05:23:24	announced	2024-10-22: Updated project metadata.

Rodriguez Carvajal A, Grishkovskaya I, Gomez Diaz C, Vogel A, Sonn-Segev A, Kushwah MS, Schodl K, Deszcz L, Orban-Nemeth Z, Sakamoto S, Mechtler K, Kukura P, Clausen T, Haselbach D, Ikeda F, The linear ubiquitin chain assembly complex (LUBAC) generates heterotypic ubiquitin chains. Elife, 10():(2021) [pubmed]

10.7554/elife.60660;

10.6019/PXD019771;

submitter keyword: E3 ubiquitin ligase/ Ester-bond linkage/ HOIL-1L/ RBR/ Ubiquitin

Fumiyo Ikeda
contact affiliation	Professor Department of Molecular and Cellular Biology Medical Institute of Bioregulation Japan
contact email	fumiyo.ikeda@bioreg.kyushu-u.ac.jp
lab head
Antonia Vogel
contact affiliation	IMP-Research Institute of Molecular Pathology
contact email	antonia.vogel@imp.ac.at
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/2021/06/PXD019771

PRIDE project URI

• PRIDE
  1. PXD019771
     1. Label: PRIDE project
     2. Name: The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains