PXD046056

PXD046056 is an original dataset announced via ProteomeXchange.

Title	Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation
Description	AMBRA1 is a tumor suppressor protein that functions as a substrate receptor of the ubiquitin conjugation system with roles in autophagy and the cell cycle regulatory network. The intrinsic disorder of AMBRA1 has thus far precluded its structural determination. To solve this problem, we analyzed the dynamics of AMBRA1 using hydrogen deuterium exchange mass spectrometry (HDX-MS). The HDX results indicated that AMBRA1 is a highly flexible protein and can be stabilized upon interaction with DDB1, the adaptor of the Cullin4A/B E3 ligase. Here, we present the cryo-EM structure of AMBRA1 in complex with DDB1 at 3.08 Å resolution. The structure shows that parts of the N- and C-terminal structural regions in AMBRA1 fold together into the highly dynamic WD40 domain and reveals how DDB1 engages with AMBRA1 to create a binding scaffold for substrate recruitment. The N-terminal helix-loop-helix motif and WD40 domain of AMBRA1 associate with the double-propeller fold of DDB1. We also demonstrate that DDB1 binding-defective AMBRA1 mutants prevent ubiquitination of the substrate Cyclin D1 in vitro and increase cell cycle progression. Together, these results provide structural insights into the AMBRA1-ubiquitin ligase complex and suggest a mechanism by which AMBRA1 acts as a hub involved in various physiological processes.
HostingRepository	PRIDE
AnnounceDate	2023-11-16
AnnouncementXML	Submission_2023-11-16_04:08:23.234.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Goran Stjepanovic
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-11 05:24:57	ID requested
⏵ 1	2023-11-16 04:08:23	announced

Dataset with its publication pending

submitter keyword: AMBRA1, cell cycle, HDX-MS, E3 ligase, Cullin4

Goran Stjepanovic
contact affiliation	Kobilka Institute of Innovative Drug Discovery, School ofMedicine, The Chinese University of Hong Kong, Shenzhen, China, 518172
contact email	goranstjepanovic@cuhk.edu.cn
lab head
Goran Stjepanovic
contact affiliation	CUHKSZ
contact email	goranstjepanovic@cuhk.edu.cn
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/2023/11/PXD046056

PRIDE project URI

• PRIDE
  1. PXD046056
     1. Label: PRIDE project
     2. Name: Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation