PXD037494 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:48:43.984.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 HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-10-17 01:31:57 | ID requested | |
1 | 2024-07-03 02:20:09 | announced | |
⏵ 2 | 2024-10-22 06:48:44 | announced | 2024-10-22: Updated project metadata. |
Publication List
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; |
Keyword List
submitter keyword: DNA repair,DNA damage response, protein assembly |
Contact List
Nevan Krogan |
contact affiliation | Department of Cellular and Molecular Pharmacology, 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037494
- Label: PRIDE project
- Name: A multi-scale map of protein assemblies in the DNA damage response