Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Parkin is an E3 ligase for the ubiquitin-like modifier Fat10 which inhibits Parkin activation and mitophagy

ABSTRACT: Parkin is an E3 ubiquitin ligase belonging to the RING-between-RING family. Mutations in the Parkin-encoding gene PARK2 are associated with familial Parkinson’s Disease. Here, we investigate the interplay between Parkin / Parkin-S65P and the inflammatory cytokine-induced ubiquitin-like modifier FAT10.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

DISEASE(S): Parkinson's Disease

SUBMITTER: Florian Stengel

LAB HEAD: Florian Stengel

PROVIDER: PXD022109 | Pride | 2021-03-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	EXP_def_ParkinS65PFat10_4_vs_ParkinFat10_2_ld20_monolinks.def	Other
	EXP_def_ParkinS65PFat10_4_vs_ParkinFat10_2_ld20_monolinks.xls	Xls
	EXP_def_ParkinS65P_3_vs_Parkin_1_ld20_monolinks.def	Other
	EXP_def_ParkinS65P_3_vs_Parkin_1_ld20_monolinks.xls	Xls
	F2010_sailerc_003.raw	Raw

Items per page:

1 - 5 of 125

Similar Datasets

To decipher an overall structure of a bacterial anti-plasmid defense system using cross-linking mass spectrometry.

Project description:The submitted data is from a BS3 crosslinked sample. The anti-plasmid defense system complex constitutes JetA, JetB, JetC, and JetD subunits. In this work, these four subunits were mixed to form a holo-subunit complex which was followed by crosslinking with isotopically/non-isotopically (1:1) mixture of BS3 reagent. The interactin subunit crosslinks were identified and this information was integrated with alphafold2 enabled models to construct an overall picture of a highly dynamic complex assembly

2022-10-06 | PXD031096 | Pride

The ubiquitin-like modifier FAT10 interferes with SUMO activation

Project description:In this study, the proteins SumoE1 and Fat10 or Fat10-AV mutant were crosslinked using the crosslinking reagent H12/D12 BS3 in order to determine specific interaction sites of Fat10 and SumoE1. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare crosslink abundances of SumoE1 in presence of Sumo as well as Sumo and Fat10 versus crosslink abundances of SumoE1 in absence of Sumo and Fat10 in order to determine the influence of Sumo and Fat10 on the structural dynamics of SumoE1.

2019-10-08 | PXD012592 | Pride

PolyQ-expansion does not alter the huntingtin-HAP40 complex

Project description:The amplification of a CAG repeat in the gene coding for huntingtin (HTT) leads to Huntington’s disease (HD). At the protein level, this translates into the expansion of a poly-glutamine (polyQ) stretch in the HTT N-terminus, which renders HTT aggregation-prone by unknown mechanisms. Here we investigate the effects of polyQ expansion on the HTT-HAP40 complex, where HTT structure is substantially stabilized. Surprisingly, our biophysical, cryo-EM and crosslinking mass spectrometry experiments reveal no major changes between 17QHTT-HAP40 (wild type), 46QHTT-HAP40 (typical polyQ length in HD patients) and 128QHTT-HAP40 (extreme polyQ length). Thus, the proposed destabilizing effect of HTT polyQ expansion may not suffice to alter the HTT-HAP40 complex, suggesting that polyQ expansion does not have a major global effect on HTT structure.

2021-03-19 | PXD018451 | Pride

iCLIP Analysis of WT, phospho-defective, and phospho-mimicking mutants of mouse Nucleolin in iKras PDAC cells

Project description:This experiment aimed to identify Nucleolin (Ncl) binding sites on a transcriptome-wide scale, by performing iCLIP in mouse iKras PDAC cells (Ying et al., 2012) transiently transfected with a mammalian expression construct encoding a wild-type (WT) myc-Ncl, a phospho-defective mutant in which S28, S34, S40, and S41 residues were mutated to A, or a phospho-mimicking mutant with these residues mutated to D. Cells transfected with an empty vector (myc-pRK5-DEST) were used as controls in the experiment.

2023-03-01 | E-MTAB-12481 | biostudies-arrayexpress

Chemical crosslinking and mass spectrometry of the human Rix1 complex

Project description:PELP1 is a scaffold protein with diverse cellular functions including its role as the central scaffold for the human Rix1 complex (PELP1, WDR18, TEX10, and SENP3). We have reconstituted the mammalian Rix1 complex and identified a sub-complex made of the conserved Rix1 domain of PELP1 and the WDR18 protein. Moreover, using Cryo-electron microscopy (cryo-EM) and aided by chemical crosslinking and mass spectrometry, we determined the structure of this PELP1 Rix1 domain complexed with WDR18.

2023-03-11 | PXD037729 | Pride

Early Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC

Project description:In this study, NAC was UV-crosslinked using the photo-crosslinking amino acid p-benzoyl-L-phenylalanine (pBPA) in order to determine specific interaction sites of the alphaNAC N-terminus in the native protein structure. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare crosslink abundances of a NAC mutant versus wild type NAC in order to determine the influence of the mutated motive on the structural dynamics of NAC.

2019-07-25 | PXD011995 | Pride

Dual FAN1 activities stabilize the HTT CAG repeat

Project description:Recent data strongly suggest HTT CAG repeat expansion drives Huntington’s disease (HD) pathogenesis and that disease development is modulated by components of the DNA damage response (DDR) pathway. FAN1 has been identified as a major HD modifier which slows expansion of the HTT CAG repeat in several cell and animal HD models. Here we show dual FAN1 activities act to inhibit repeat expansion. A highly conserved SPYF motif in the FAN1 N-terminus is required for an MLH1 interaction, which slows expansion, with FAN1 nuclease activity also contributing towards repeat stabilisation. Our data supports a model where FAN1 binds MLH1, restricting its recruitment by MSH3 and the formation of the functional DNA mismatch repair (MMR) complex believed to promote CAG repeat expansion. FAN1 nuclease activity functions either concurrently or following MMR activity to maintain repeat stability. These data highlight a potential avenue for HD therapeutics in attenuating somatic expansion.

2022-02-16 | PXD023221 | Pride

The modulation of CHD4 nucleosome remodelling activity by auxiliary domains suggests unifies mechanistic aspects of chromatin remodelling across enzyme families

Project description:We determine the impact of auxiliary domains on the nucleosome sliding activity of CHD4. This dataset comprises the crosslinking mass spectrometry data we reported.

2023-03-11 | PXD033633 | Pride

An Mtw1 C terminal motif is cruical for cooperative outer kinetochore assembly in budding yeast

Project description:We employed chemical crosslinking and mass spectrometry on in vitro reconstituted outer kinetochore KMN network.

2020-09-30 | PXD011775 | Pride

Conformational rearrangements upon start codon recognition in human 48S translation initiation complex

Project description:Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1A, eIF1, eIF2–GTP–Met-tRNAiMet, eIF3, eIF4A and eIF4B. The ‘open’ 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The ‘closed’ form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast.

2022-06-09 | PXD031985 | Pride

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