Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

AP-MS_XL experiment to characterize YAP1/LATS/PTPN14 complex

ABSTRACT: In this project we investigated the topological composition of ternary complex PTPN14/LATS1/PTPN14. For this purpose, we performed affinity purification with Strep tag of Strep-HA YAP1 and subsequent XL reaction.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Federico Uliana

LAB HEAD: Dr. Matthias Gstaiger

PROVIDER: PXD039440 | Pride | 2023-03-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	mini_rev_shuffle.fasta	Fasta
	results_no_filt.csv	Csv
	sample_annotation.xlsx	Xlsx
	ulianaf_C1604_169.c.mzXML	Mzxml
	ulianaf_C1604_170.c.mzXML	Mzxml

Items per page:

1 - 5 of 18

Similar Datasets

Targeted analysis of PTPN14, YAP1, LATS1 and GFP SH-tagged pulldown

Project description:Targeted analysis of YAP1, LATS1 and PTPN14 interactome

2023-03-04 | PXD032221 | Pride

Identification of XL peptides in Bik1 variants and different conditions

Project description:Identification of crosslinks in Bik1 variants and different conditions (phase separation, soluble, supernatant, pellet).

2025-01-06 | PXD050929 | Pride

Identification of Bik1 XL peptides (DSS)

Project description:Effect of different DSS concentrations and varying collision energy on the number of identified crosslinks.

2025-01-06 | PXD050928 | Pride

26S proteasome crosslinking mass spectrometry data for mi-filter

Project description:In this project we are describing a novel mono- and intralink filter (mi-filter) that is applicable to any kind of crosslinking data and workflow. It stipulates that only proteins for which at least one monolink or intra-protein crosslink has been identified within a given dataset are considered for an inter-protein cross-link and therefore participate in a PPI. We show that this simple and intuitive filter has a dramatic effect on all types of crosslinking-data ranging from single protein complexes, over medium-complexity affinity enrichments to proteome-wide settings and significantly improves false-discovery rates for inter-protein links in all types of XL-MS data.

2022-12-14 | PXD031215 | Pride

XL-MS of 5S RNP preribosomal complexes

Project description:The 5S RNP is assembled from its three components (5S rRNA, Rpl5/uL18, and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is disturbed, a free 5S RNP can enter the MDM2–p53 pathway to regulate cell cycle and apoptotic signaling. Here we reconstitute and determine the cryo-EM structure of the conserved hexameric 5S RNP with fungal or human factors. This reveals how the nascent 5S rRNA associates with the initial nuclear import complex Syo1–uL18–uL5, and upon further recruitment of two nucleolar factors Rpf2–Rrs1 develops into the 5S RNP precursor that can assemble into the pre-ribosome. In addition, we elucidate the structure of another 5S RNP intermediate, carrying the human ubiquitin ligase Mdm2, which unraveled how this enzyme can be sequestered from its target substrate p53. Our data provide molecular insight into how the 5S RNP can mediate between ribosome biogenesis and cell proliferation.

2023-06-13 | PXD040087 | Pride

Cross-linking MS data of CtNup82-Y complex

Project description:XL-MS Data of the in vitro reconstituted CtNup82-Y complex.

2018-10-17 | PXD007043 | Pride

Structure of the Cohesin Loader Scc2-Scc4 and its Binding to a Folded Cohesin

Project description:The functions of cohesin are central to genome integrity, chromosome organization, and transcription regulation through its prevention of premature sister-chromatid separation and the formation of DNA loops. The loading of cohesin onto chromatin depends on the Scc2-Scc4 complex, however, little is known about how it stimulates the cohesin loading activity. Here we determine the large “hook” structure of Scc2 responsible for catalyzing cohesin loading. We identify key Scc2 surfaces that are crucial for DNA binding and for cohesin loading in vivo. Using previously determined structures and modeling, we derive a pseudo-atomic structure of the full-length Scc2-Scc4 complex. Finally, our crosslinking and electron microscopy analyses reveal that Scc2-Scc4 utilizes its modular structure to make multiple contacts with a folded cohesin at an interface created by the cohesin head-hinge interaction.

2017-01-11 | PXD004692 | Pride

MS Analysis In vivo treatment of YAP1 SH tagged with phosphatase inhibitors

Project description:Investigation of YAP1 interactome plasticity via APMS

2023-03-04 | PXD032218 | Pride

Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains

Project description:Influenza virus polymerase transcribes or replicates the segmented RNA genome (vRNA) into respectively viral mRNA or full-length copies and initiates RNA synthesis by binding the conserved 3' and 5' vRNA ends (the promoter). In recent structures of promoter-bound polymerase, the cap-binding and endonuclease domains are configured for cap snatching, which generates capped transcription primers. Here, we present a FluB polymerase structure with a bound complementary cRNA 5' end that exhibits a major rearrangement of the subdomains within the C-terminal two-thirds of PB2 (PB2-C). Notably, the PB2 nuclear localization signal (NLS)- containing domain translocates ~90 A ̊ to bind to the endonuclease domain. FluA PB2-C alone and RNA-free FluC polymerase are similarly arranged. Biophysical and cap-dependent endonuclease assays show that in solution the polymerase explores different conformational distributions depending on which RNA is bound. The inherent flexibility of the polymerase allows it to adopt alternative conformations that are likely important during polymerase maturation into active progeny RNPs.</br></br>Extra contact information:</br><a href="mailto:cusack@embl.fr">Stephen Cusack</a>, EMBL Grenoble Outstation, Unit of Virus Host-Cell Interactions, France ( corresponding author and lab head )

2016-01-04 | PXD002234 | Pride

Structure of the AAA-ATPase Drg1 during extraction of Rlp24 from pre-60S particles

Project description:The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures showing a hand-over-hand translocation mechanism of Drg1 and additional XL-MS data on positioning of Drg1 on pre-60S particles.

2022-10-14 | PXD032098 | Pride