Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thianthrenium chemistry for identification of protein−protein interactions in cells

ABSTRACT: The dataset contains raw data, peakfiles used for the database searches, as well as search results for the crosslinking LC-MS/MS data

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Kostiantyn Bohdan

LAB HEAD: Tobias Ritter

PROVIDER: PXD066251 | Pride | 2025-11-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HSapiens.fasta	Fasta
	MPIKF_BB_652_16_1_1.mgf	Mgf
	MPIKF_BB_652_16_1_2.mgf	Mgf
	MPIKF_BB_652_16_1_3.mgf	Mgf
	MPIKF_BB_652_16_1_4.mgf	Mgf

Items per page:

1 - 5 of 35

Similar Datasets

Condensin II Activation by the centromeric protein M18BP1

Project description:Condensin I and condensin II promote drastic spatial compaction (condensation) of the genome upon mitotic entry. Condensin I binds chromatin only after dissolution of the nuclear envelope in prophase. Conversely, condensin II is nuclear throughout the cell cycle and initiates chromosome condensation. Previous studies demonstrated that MCPH1 inhibits condensin II to prevent chromosome condensation during interphase. Mechanisms that promote condensin II activation in early mitosis likely exist but are currently unknown. Through genetic and proteomic approaches, we identify M18BP1, a protein previously associated with centromere identity, as a factor required for condensin II localization to chromatin during mitosis. To activate and localize condensin II, M18BP1 directly binds the CAP-G2 subunit. M18BP1 and MCPH1 compete for CAP-G2 binding, and CDK1 phosphorylation promotes replacement of MCPH1 with M18BP1 to activate condensin II upon mitotic entry. Our results identify a fundamental and evolutionarily conserved mechanism of condensin II activation.

2025-07-09 | PXD051886 | Pride

Crosslinking mass spectrometry analysis of 𝛾TuRC complex

Project description:The 𝛾-tubulin ring complex (𝛾TuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. To understand the molecular basis of microtubule nucleation, we investigate the structure of 𝛾TuRC using crosslinking mass spectrometry.

2021-01-27 | PXD018106 | Pride

Cryo-EM structures of the Plant Augmin reveal its intertwined coiled-coil assembly, antiparallel dimerization and NEDD1 binding mechanisms

Project description:Microtubule (MT) branch nucleation is fundamental for building parallel MT networks in eukaryotic cells. In plants and metazoans, MT branch nucleation requires Augmin and NEDD1 proteins which bind along MTs and then recruit and activate the gamma-tubulin ring complex (g-TuRC). Augmin is a fork-shaped assembly composed of eight coiled-coil subunits, while NEDD1 is a b-propellor protein that bridges across MTs, Augmin, and g-TuRC during MT branch nucleation. Here, we reconstitute hetero-tetrameric and hetero-octameric Arabidopsis thaliana Augmin assemblies, resolve their subunit interactions using crosslinking mass spectrometry and determine 3.7 to 7.3-Å cryo-EM structures for the V-junction and extended regions of Augmin. These structures allowed us to generate a complete de novo plant Augmin model that reveals the long-range multi coiled-coil interfaces that stabilize its 40-nm hetero-octameric fork-shaped organization. We discovered the dual calponin homology (CH) domain forming its MT binding site at one end of its V-junction can assume open and closed conformations. We determined a 12-Å dimeric Augmin cryo-EM structure revealing Augmin undergoes anti-parallel dimerization through two conserved surfaces along Augmin’s extended region. We reconstituted the NEDD1 b-propellor with Augmin revealing it directly binds into its V-junction and enhances Augmin dimerization. Our studies suggest that cooperativity between the Augmin dual CH domains and NEDD1 binding site may regulate Augmin V-junction dual binding to MT lattices. This unique V-shaped dual binding and organization anchors Augmins along MTs generating a platform to recruit g-TuRC and activate branched MT nucleation.

2025-10-31 | PXD065516 | Pride

Characterisation of BiP-GRP94-HT2 interaction

Project description:Characterization of the interaction of BiP-GRP94 in the presence and absence of HT2 using cross linking with DSBU and subsequent analysis of cross linked peptides by LC-MS/MS

2025-07-14 | PXD059917 | Pride

Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA

Project description:Prokaryotic Argonaute proteins (pAgos) from the long-A clade are stand-alone immune systems that use small interfering (si)DNA guides to recognize and cleave invading plasmid and virus DNA. Certain long-A pAgos are co-encoded with accessory proteins with unknown functions. Here, we show that cyanobacterial long-A pAgos act in conjunction with Argonaute-associated Cas4 family enzyme 1 (ACE1). Structural and biochemical analyses reveal that ACE1-associated pAgos mediate siDNA-guided DNA interference, akin to stand-alone pAgos. ACE1 is structurally homologous to the nuclease domain of bacterial DNA repair complexes and acts as a single-stranded DNA endonuclease that processes siDNA guides. pAgo and ACE1 form a heterodimeric APACE1 complex, which modulates ACE1 activity. While ACE1-associated pAgos alone interfere with plasmids and bacteriophages, plasmid interference is boosted when pAgo and ACE1 are co-expressed. Our study reveals that pAgo-mediated immunity is enhanced by accessory proteins and broadens our mechanistic understanding of how pAgo systems interfere with invading DNA.

2025-04-15 | PXD060946 | Pride

In-cell architecture of an active transcription-translation complex

Project description:Structural biology performed inside cells can capture molecular machines in action within their native context. Here we develop an integrative in-cell structural approach using the genome-reduced human pathogen Mycoplasma pneumoniae. We combine whole-cell crosslinking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at sub-nanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpoint NusA at the interface between the ribosome and a NusG-bound elongating RNAP, and propose it could mediate transcription-translation coupling. Transcription inhibition stalls and rearranges the expressome, whereas translation inhibition dissociates it, demonstrating that the elongating expressome architecture requires active translation and transcription within the cell.

2020-07-30 | PXD017695 | Pride

Crosslinking/mass spectrometry analysis of Human Separase-Scc1-fusion and cohesin SMC1/SMC3 complexes

Project description:In this study, we employed the photoactivatable crosslinker (sulfo-SDA) to investigate protein-protein interaction between human Separase-Scc1 fusion protein and SMC1/SMC3 cohesin subunits complex in the presence of DNA.

2025-08-28 | PXD061667 | Pride

STRUCTURE OF APOLIPOPROTEIN B100 BOUND TO LOW-DENSITY LIPOPROTEIN RECEPTOR (SDA ASPN XL DATA)

Project description:Apolipoprotein B100 (apoB100) is the main structural protein on Low-density Lipoproteins (LDL) and is the principal ligand for the LDL receptor (LDLR). Because the tertiary structure of apoB100 on LDL has not been determined, the detailed molecular interaction between apoB100 and LDLR is unknown. Here we present the structures of LDL bound to the LDLR and an apoB100 nanobody complex at 4.18Å resolution and a second LDL-LDLR interface at 4.83Å resolution.

2024-12-06 | PXD051588 | Pride

STRUCTURE OF APOLIPOPROTEIN B100 BOUND TO LOW-DENSITY LIPOPROTEIN RECEPTOR (SDA XL DATA)

2024-12-06 | PXD051423 | Pride

Structural analysis of the PTEN:P-Rex2 signaling node reveals how cancer-associated mutations coordinate to hyperactivate Rac1

Project description:The PTEN:P-Rex2 complex is a commonly mutated signaling nodes in metastatic cancer. The dual-specificity phosphatase PTEN canonically functions as a tumour suppressor by hydrolysing PI(3,4,5)P3 to PI(4,5)P2 to inhibit PI3K-AKT signaling. P-Rex2 is a RhoGTPase guanine nucleotide exchange factor activated by both Gβγ and PI(3,4,5)P3 downstream of G protein-coupled receptor and receptor tyrosine kinase signaling. Assembly of the PTEN:P-Rex2 complex inhibits the activity of both proteins, and its dysregulation can drive PI3K-AKT signaling and cell proliferation. However, structural insights into both PTEN:P-Rex2 complex assembly and its dysregulation by cancer-associated mutations remain limited. Here, using crosslinking mass spectrometry and functional studies, we provide mechanistic insights into PTEN:P-Rex2 complex assembly and co-inhibition. PTEN is anchored to P-Rex2 by interactions between the PTEN C-terminal tail PDZ-interacting motif and the second PDZ domain of P-Rex2. This interaction bridges PTEN across the P-Rex2 surface, occluding PI(3,4,5)P3 hydrolysis. Conversely, PTEN both allosterically promotes an autoinhibited P-Rex2 conformation and occludes Gβγ binding. These insights allow us to define a new gain-of-function class of cancer mutations within the PTEN:P-Rex2 interface that uncouples PTEN inhibition of Rac1 signaling. In addition, we observe synergy between PTEN deactivating and P-Rex2 truncation mutations that combine to drive Rac1 activation to a greater extent than either single mutation alone.

2022-08-12 | PXD021126 | 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