PXD028064-1

PXD028064 is an original dataset announced via ProteomeXchange.

Title	A multi-scale map of protein assemblies in the DNA damage response
Description	The DNA damage response (DDR) ensures error-free genome replication and transcription and is disrupted in numerous pathologies including cancer, inflammation and aging1–5. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into protein assemblies and complexes, some of which are constitutive, some which emerge de novo or are remodeled in DNA damaging conditions6. Here we integrate multi-conditional protein interaction networks with diverse multi-omics datasets to create a comprehensive map of DDR protein assemblies at multiple scales of analysis. This DNA damage response assembly map (DDRAM) encompasses 336 proteins, of which 57 (17%) are newly implicated in sensing or repair of DNA damage. We establish a requirement for three such factors in homologous recombination, the lipid chaperone FABP5, the actin-depolymerizing factor GSN, and the galectin LGALS7 as part of the BRCA2/PALB2 DNA repair complex. Another 204 (61%) proteins are known DDR factors assigned more specific functions. We find that single-strand DNA repair (SSR) factors segregate into a collection of 18 nested assemblies, which mirrors the function and dynamic aggregation of these factors at sites of DNA damage. One of these factors, CHTF18, localizes in a PARP-dependent manner with dynamics distinct from those in other SSR assemblies. The map is available at ccmi.org/ddram for interactive visualization, query and download.
HostingRepository	PRIDE
AnnounceDate	2024-07-03
AnnouncementXML	Submission_2024-07-03_02:50:53.671.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Minkyu Kim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-23 06:36:48	ID requested
⏵ 1	2024-07-03 02:50:54	announced
2	2024-10-22 06:48:42	announced	2024-10-22: Updated project metadata.

Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T, A multi-scale map of protein assemblies in the DNA damage response. Cell Syst, 14(6):447-463.e8(2023) [pubmed]

10.1016/j.cels.2023.04.007;

submitter keyword: Human, Protein assembly map, DNA damage response

Nevan Krogan
contact affiliation	University of California San Francisco
contact email	minkyu.kim@ucsf.edu
lab head
Minkyu Kim
contact affiliation	University of California San Francisco
contact email	minkyu.kim@ucsf.edu
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/2024/07/PXD028064

PRIDE project URI

• PRIDE
  1. PXD028064
     1. Label: PRIDE project
     2. Name: A multi-scale map of protein assemblies in the DNA damage response