Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2

ABSTRACT: Otu2-driven deubiquitylation of ribosomal protein eS7 impacts translational efficiency. Here, authors provide the molecular basis for recognition of monoubiquitinated eS7 on 40S and give mechanistic insights into Otu2’s role in translation reset. In this context quantitative mass spectrometry analyses of OTU2 and UBP3 pulldowns were performed.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Thomas Fröhlich

LAB HEAD: Thomas Fröhlich

PROVIDER: PXD041573 | Pride | 2023-05-13

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Obp3_TEV_5_R1.raw	Raw
	Obp3_TEV_5_R2.raw	Raw
	Obp3_TEV_6_R1.raw	Raw
	Obp3_TEV_6_R2.raw	Raw
	Obp3_TEV_7_R1.raw	Raw

Items per page:

1 - 5 of 32

Publications

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.

Ikeuchi Ken K Ivic Nives N Buschauer Robert R Cheng Jingdong J Fröhlich Thomas T Matsuo Yoshitaka Y Berninghausen Otto O Inada Toshifumi T Becker Thomas T Beckmann Roland R

Nature communications 20230512 1

In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome ...[more]

PMID: 37169754

Similar Datasets

Mus musculus

Project description:RETRACTED BY AUTHORS

| PRJNA92487 | ENA

Crosslinking mass spectrometry (CLMS) analysis of monoubiquitinated FANCD2-FANCI complex

Project description:Vertebrate DNA crosslink repair excises toxic replication-blocking DNA crosslinks. Numerous factors involved in crosslink repair have been identified, and mutations in their corresponding genes cause Fanconi anemia (FA). A key step in crosslink repair is monoubiquitination of the FANCD2-FANCI heterodimer, which then recruits nucleases to remove the DNA lesion. In this study, monoubiquitinated FANCD2-FANCI complex was characterized using crosslinking mass spectrometry in order to provide in sights into the 3D structure of the complex.

2020-03-09 | PXD017020 | Pride

Homo sapiens

Project description:Reproduction of reset cell

| PRJNA277636 | ENA

Transcriptome profiling of SOD1 mutant ALS model motor neurons.

Project description:Recent genetic studies of ALS patients have identified several forms of ALS that are associated with mutations in RNA binding proteins. In animals or cultured cells, such defects broadly affect RNA metabolism. This raises the question of whether all forms of ALS have general effects on RNA metabolism. We tested this hypothesis in a mouse model of ALS that is transgenic for a human disease-causing mutation in the enzyme superoxide dismutase 1 (SOD1). We analyzed RNA from laser-captured spinal cord motor neuron cell bodies of the mutant SOD1 strain, comparing the RNA profile with that from a corresponding wild-type SOD1 transgenic strain. We prepared the samples from animals that were presymptomatic, but which manifested abnormalities at the cellular level that are seen in ALS, including aggregation of the mutant protein in motor neuron cell bodies and defective morphology of neuromuscular junctions, the connections between neuron and muscle. We observed only minor changes in the level and splicing of RNA in the SOD1 mutant animals as compared with wild-type, suggesting that mutant SOD1 produces the toxic effects of ALS by a mechanism that does not involve global RNA disturbance. RNA-Seq of laser microdissection of motor neuron bodies from two biological replicates each of SOD1 YFP (wildtype 592) and SOD1 G85R YFP (737) transgenic mice.

2012-12-04 | E-GEOD-38820 | biostudies-arrayexpress

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements

Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.

2010-06-16 | E-GEOD-19371 | biostudies-arrayexpress

Ubiquitinated histone H2A mapping in Drosophila ML-DmBG3 cells

Project description:Monoubiquitinated histone H2A produced by the Sce/Ring subunit of the Polycomb Repressive Complex 1 (PRC1) was mapped genome-wide in Drosophila ML-DmBG3 cells using chromatin immunoprecipitation followed by hybridization to Affymetrix tiling arrays. ML-DmBG3 chromatin immunoprecipitated with anti-histone H2AK119ub antibody and matching input chromatin were amplified, labeled and hybridized to Affymetrix tiling arrays to determine the locations of ubiquitinated H2A genome-wide.

2013-08-09 | E-GEOD-49634 | biostudies-arrayexpress

Ubiquitinated histone H2A mapping in Drosophila ML-DmBG3 cells

2013-08-09 | GSE49634 | GEO

DNA framework-engineered chimeras platform enables selectively targeted protein degradation

Project description:In the target protein degradation field, proteomics has been widely used to demonstrate the selectivity of designed degraders. The authors perform a proteomics analysis on one representative degrader to demonstrate its selectivity more broadly.

2023-06-27 | PXD042665 | Pride

Hybrid_Poplar_H11-11_Leaves_Local_Stress_Response_DataSet2

Project description:We investigated the transcriptional response of hybrid poplar (Populus trichocarpa x deltoides) leaves to methyl jasmonate treatment over a 24 hour time course. Experiments were conducted using clonal trees under greenhouse conditions at the University of British Columbia. We used the 15.5K poplar cDNA microarray platform previously described by Ralph et al. (Molecular Ecology 2006, 15:1275-1297). Differentially expressed genes were determined using three criteria: fold-change between methyl jasmonate-treated and tween-treated control leaves > 1.5-fold, P value < 0.05 and Q value < 0.05. This study identified > 1,000 differentially expressed genes in response to methyl jasmonate treatment. A factorial hybridization design was chosen to assess gene expression between tween-treated control leaves, and leaves subjected to methyl jasmonate treatment. For each tree, all but the lowest five mature leaves were covered with a light-weight plastic bag and then sprayed with either methyl jasmonate or tween, the solvent control. Leaves were harvested 2, 6 or 24 hours after the initiation of each treatment and total RNA was individually isolated from each tree. For each treatment and time point, equal amounts of total RNA were combined from each of the five biological replicate trees prior to cDNA microarray analysis. A total of 18 hybridizations were performed to directly compare total RNA from methyl jasmonate-treated and tween-treated control leaves at each time point, as well as among methyl jasmonate-treated leaves across time points, with dye balance.

2008-12-30 | E-GEOD-14039 | biostudies-arrayexpress

Transcription profiling of Wistar rat preconditioned hearts either perfused alone or subjected to ischemia and then reperfused

Project description:Isolated perfused rat hearts exposed to isoflurane or ischemic preconditioning, a subgroup followed by 40 minutes of ischemia and 3 hours of reperfusion. Exact protocol available from the authors.

2007-11-01 | E-GEOD-1616 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data