PXD079072

PXD079072 is an original dataset announced via ProteomeXchange.

Title	A dual-anchoring mechanism for the hemimethylated CG-guided histone ubiquitylation
Description	Maintenance of plant CG DNA methylation is critically regulated by VIM proteins, a family of SRA domain-containing E3 ligases that read hemimethylated CG (hemiCG) sites and modulate the MET1-mediated DNA methylation on chromatin. How VIM proteins bridge the hemiCG readout with their ubiquitylation activity remains unclear. Here we report the structure-function characterization of VIM1-mediated ubiquitylation on hemiCG-containing nucleosomes, revealing H3 and H4 both as the substrates of VIM1. We find that VIM1 is anchored to nucleosome via both the SRA and RING domains, with the interaction between the RING2 domain and H2A-H2B acidic patch important for the nucleosome tethering and the SRA-hemiCG interaction critical for enzymatic catalysis. Formation of a helical bundle between the RING1 and RING2 domains of VIM1 further creates a platform for cooperative VIM1-E2-nucleosome binding. Such a dual nucleosome anchoring by the SRA and RING modules underpins hemiCG-dependent VIM1-substrate assembly, permitting persistent yet context- dependent H3/H4 ubiquitylation.
HostingRepository	PRIDE
AnnounceDate	2026-05-30
AnnouncementXML	Submission_2026-05-29_18:08:09.229.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhongwen Cao
SpeciesList	scientific name: Xenopus laevis (African clawed frog); NCBI TaxID: NEWT:8355;
ModificationList	acetylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2026-05-29 17:22:28	ID requested
⏵ 1	2026-05-29 18:08:09	announced

Dataset with its publication pending

submitter keyword: Ubiquitination,DNA methylation, Propionylation, LC-MS/MS

Dr.Yinsheng Wang, Dr.Jikui Song
contact affiliation	University of California, Riverside
contact email	jikui.song@ucr.edu
lab head
Zhongwen Cao
contact affiliation	University of California, Riverside
contact email	zcao037@ucr.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD079072
     1. Label: PRIDE project
     2. Name: A dual-anchoring mechanism for the hemimethylated CG-guided histone ubiquitylation