Browse
Submit Data
Databases
API
Help

Dataset Information

164 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-linking MS data of CtNup82-Y complex

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

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Chaetomium Thermophilum

SUBMITTER: Alexander von Appen

LAB HEAD: Martin Beck

PROVIDER: PXD007043 | Pride | 2018-10-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

A short linear motif in scaffold Nup145C connects Y-complex with pre-assembled outer ring Nup82 complex.

Teimer Roman R Kosinski Jan J von Appen Alexander A Beck Martin M Hurt Ed E

Nature communications 20171024 1

Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs), which are formed from multiple copies of ~30 different nucleoporins (Nups) and inserted into the double nuclear membrane. Many of these Nups are organized into subcomplexes, of which the Y-shaped Nup84 complex is the major constituent of the nuclear and cytoplasmic rings. The Nup82-Nup159-Nsp1 complex is another module that, however, is only assembled into the cytoplasmic ring. By means of crosslinking mass spectrometry, b ...[more]

PMID: 29062044

Similar Datasets

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

Crosslinking-MS dataset of the TFIIIC subcomplex tauA with Brf1 and TBP

Project description:Identification of crosslinks between the subunits tau131, tau95, tau55, Brf1 and TBP

2020-12-04 | PXD018232 | Pride

Crosslinking mass spectrometry of yeast Pol I pre-initiation complex

Project description:In eukaryotic cells, ribosomal RNA is transcribed by RNA polymerase I (Pol I). To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC). In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3 and Core Factor (CF) composed of subunits Rrn6, Rrn7 and Rrn11. We have determined the cryo-EM structure of a 18-subunit yeast Pol I complex together with CF, Rrn3 and transcription scaffold. To aid in modeling the structure based on the cryo-EM map, we performed crosslinking mass spectrometry.

2017-07-31 | PXD006510 | Pride

Architecture of the yeast Elongator complex

Project description:The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2 and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.

2016-12-20 | PXD005251 | 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

Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex

Project description:Deregulation of the ubiquitin ligase E6AP is causally linked to the development of human disease, including cervical cancer. In complex with the E6 oncoprotein of human papillomaviruses, E6AP targets the tumor suppressor p53 for degradation, thereby contributing to carcinogenesis. Moreover, E6 acts as a potent activator of E6AP by a yet unknown mechanism. However, structural information explaining how the E6AP-E6-p53 enzyme-substrate complex is assembled, and how E6 stimulates E6AP, is largely missing. We therefore developed and applied different approaches in structural mass spectrometry to show that binding of E6 induces conformational rearrangements in E6AP, which result in the positioning of E6 and p53 in the immediate vicinity of the catalytic centre of E6AP. Our data provides structural and functional insights into the dynamics of the full-length E6AP-E6-p53 enzyme-substrate complex and reveals how E6 can both stimulate the ubiquitin ligase activity of E6AP and facilitate the transfer of ubiquitin from E6AP onto p53.

2018-10-23 | PXD010002 | Pride

The COMA complex plays a role in positioning Ipl1 activity proximal to Cse4 nucleosomes

Project description:Kinetochores are macromolecular protein complexes that ensure accurate chromosome segregation by linking chromosomes to spindle microtubules and integrating safeguard mechanisms. In yeast, the inner kinetochore, also known as Constitutive Centromere Associated Network (CCAN), is specifically established at point centromeres and has been implicated in contributing to Aurora-BIpl1 function. In an attempt to gain a more detailed picture of the budding yeast kinetochore architecture, crosslink-guided in vitro reconstitution revealed novel direct interactions of the inner kinetochore assembled on Cse4CENP-A nucleosomes. The Ame1/Okp1CENP-U/Q heterodimer selectively bound Cse4CENP-A nucleosomes through the Cse4 N-terminus, providing an explanation for the essential role of the COMA complex in budding yeast. Moreover, the Sli15/Ipl1 core chromosomal passenger complex was found to directly interact with COMA in vitro, suggesting a hitherto unknown role of the COMA complex in establishing biorientation. In line with this finding, in vivo artificial tethering of Sli15 to inner kinetochore proteins rescued synthetically lethal subunit deletion phenotypes in a Sli15 centromere targeting deficient mutant. This study reveals characteristics of the inner kinetochore architecture assembled at point centromeres and its implications on chromosomal passenger complex function.

2019-04-12 | PXD011236 | Pride

Hierarchical antagonistic regulatory elements in the TRPV4 intrinsically disordered N-terminus modulate lipid binding and channel activity through transient long-range interactions

Project description:Intrinsically disordered regions (IDRs) are important for the functional regulation of membrane receptors. Among the TRP Vanilloid channels involved in thermo- and osmosensation, TRPV4 features the largest N-terminal IDR of ~150 residues. Here, we elucidate the structural ensemble of the TRPV4 IDR through an integrated structural biology approach. Novel structural and functional properties can be assigned to distinct IDR regions. Along the length of the entire IDR, a hierarchical interaction network of structurally and functionally coupled antagonistic regulatory modules can be mapped. Long-range transient crosstalk between these regulatory elements mediates channel responses to osmotic stimuli. Most notably, a highly conserved regulatory patch in the N-terminal IDR asserts dominant negative control over lipid binding and channel activity by acting on a sensitizing PIP2 binding site in the C-terminal IDR. This work demonstrates the importance of IDRs and “IDR cartography” for understanding TRP channel function and regulation.

2023-08-01 | PXD038153 | 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

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

Project description: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.

2021-03-05 | PXD022109 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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