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ProteomicsThe Human RNA-Binding Proteome and Its Dynamics during Translational Arrest
The data presented here was produced using XRNAX - a novel extraction method for protein-crosslinked RNA from UV-crosslinked cells. We apply XRNAX for three proteomic downstream applications. First, we purify ribonucleotide-crosslinked peptides from XRNAX extracts and use their identification as dir...
ORGANISM(S): Homo sapiens (Human) 
2018-12-06 | PXD010520 | Pride
Uv-crosslinking Nucleotide-crosslinked peptides Xrnax Protein-crosslinked rna extraction Rna-binding proteins Arsenite stress Translational arrest Human rna-binding proteome Ribophagy 
UnknownDrug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae.
Not available
S-EPMC9541285 | biostudies-literature
ProteomicsNucleotide independant as well as ATP-hydrolysis driven steps of Rea1 Linker remodelling drive the removal of assembly factors from pre-ribosomal particles: PhoX cross-linking of Rea1 in presence of ATPgS, AMP-PNP or Apo state.
The ribosome maturation factor Rea1 (or Midasin) catalyses the removal of assembly factors from large ribosomal subunit precursors and to promotes their export from the nucleus to the cytosol. Rea1 consists of nearly 5000 amino-acid residues and belongs to the AAA+ protein family. It consists of a r...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-07-29 | PXD053636 | Pride
Cross-linking mass spectrometry Structural biology Structural proteomics 
ProteomicsIdentification of 60S pre-rRNA binding sites of human GNL3L GTPase
We reveal that the GNL3 paralogue GTPase, GNL3L, associates with pre-ribosomes. We map RNA contact sites on GNL3L as well as GNL3L binding sites on pre-rRNAs. Lack of GNL3L impairs synthesis of the 60S rRNAs and expression of GTPase inactive GNL3L causes defects in early steps of pre-rRNA processing...
ORGANISM(S): Homo sapiens (Human) 
2026-03-05 | PXD067606 | Pride
Human Gtpase Gnl3l 60s rrna Rna-protein crosslinking 
ProteomicsStructure of the human FERRY Rab5 effector complex
Long-range mRNA transport is crucial for the spatio-temporal regulation of gene expression, and its malfunction is linked to neurological disorders. The pentameric FERRY Rab5 effector complex is the molecular link between mRNA and the early endosome in mRNA intracellular distribution. Here, we deter...
ORGANISM(S): Homo sapiens (Human) 
2023-10-23 | PXD034875 | Pride
Human Structure 
ProteomicsInter- and Intra-Molecular Interactions of The Arabidopsis Plasma Membrane Proton Pump Revealed Using a Mass Spectrometric-Cleavable Crosslinker
In plants and fungi, the plasma membrane proton pump (H+-ATPase) establishes an electrochemical gradient across the plasma membrane which serves as the driving force for the secondary transport of ions and nutrients across the cell membrane. This is an essential enzyme that functions in many importa...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Saccharomyces cerevisiae (Baker's yeast) 
2023-06-01 | PXD018219 | Pride
Arabidopsis Plasma membrane protein pump Metabolic labeling Dsso Crosslinking 
ProteomicsIntensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links
Rescoring of protein-RNA cross-links using retention time and intensity prediction.
ORGANISM(S): Escherichia coli 
2025-11-24 | PXD048145 | Pride
Lc-msms Protein-rna cross-links Bottom-up proteaomics 
ProteomicsMapping RNA interactions of human ATRX with RepA fragment of Xist
Heterochromatin in the eukaryotic genome is rigorously controlled by the concerted action of protein factors and RNAs. Here, we investigate the RNA binding function of ATRX, a chromatin remodeler with roles in silencing of repetitive regions of the genome and in recruitment of the polycomb repressi...
ORGANISM(S): Homo sapiens (Human) 
2020-03-09 | PXD017806 | Pride
Rbrid  rna-protein interactions  rna-binding 
ProteomicsThe cochaperone CHIP marks Hsp70- and Hsp90-bound substrates for degradation through a very flexible mechanism
Some molecular chaperones are involved not only in assisting the folding of proteins but also, given appropriate conditions, in their degradation. This is the case of Hsp70 and Hsp90, which direct their bound substrate to degradation through ubiquitination in concert with the cochaperone CHIP –an E...
ORGANISM(S): Homo sapiens (Human) 
2019-03-07 | PXD009756 | Pride
Shotgun Dsso Crosslinking 
ProteomicsHuman U2OS DNApk GLASS-ChIP LC-MS/MS
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5ʹ strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site—a role we postulate is played by DNA-dependent protei...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD045033 | Pride
Human U2os Glass-chip Dnapk Lc-ms/ms 
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