Browse
Submit Data
Databases
API
Help

Dataset Information

114 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-linking mass spectrometric analysis of Ska-MT interactions

ABSTRACT: This project is about characterizing the interaction of the MT-binding domains (MTBD) of the human Ska complex with MTs by cross-linking mass spectrometry

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Juan Zou

LAB HEAD: Juri Rappsilber

PROVIDER: PXD003502 | Pride | 2016-01-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Zou_Rappsilber_JP_SkaComplex.xlsx	Xlsx
	Zou_Rappsilber_JP_SkaComplex.zip	Other
	Zou_Rappsilber_JP_SkaComplex_F1.raw	Raw
	Zou_Rappsilber_JP_SkaComplex_F2.raw	Raw
	Zou_Rappsilber_JP_SkaDomainComplex.xlsx	Xlsx

Items per page:

1 - 5 of 10

Publications

Structural basis for microtubule recognition by the human kinetochore Ska complex.

Abad Maria Alba MA Medina Bethan B Santamaria Anna A Zou Juan J Plasberg-Hill Carla C Madhumalar Arumugam A Jayachandran Uma U Redli Patrick Marc PM Rappsilber Juri J Nigg Erich A EA Jeyaprakash A Arockia AA

Nature communications 20140101

The ability of kinetochores (KTs) to maintain stable attachments to dynamic microtubule structures ('straight' during microtubule polymerization and 'curved' during microtubule depolymerization) is an essential requirement for accurate chromosome segregation. Here we show that the kinetochore-associated Ska complex interacts with tubulin monomers via the carboxy-terminal winged-helix domain of Ska1, providing the structural basis for the ability to bind both straight and curved microtubule struc ...[more]

PMID: 24413531

Similar Datasets

Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo

Project description:As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting and folding factors. Here we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone Trigger Factor (TF) reveal that, while TF can interact with many polypeptides, Î²-barrel outer membrane proteins are the most prominent substrates. Loss of TF leads to broad outer membrane defects and premature, cotranslational protein translocation. While in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting ad folding factors. Examination of translation in the Gram-negative bacterium Escherichia coli, as well as an analysis of the interactions between nascent chains and the molecular chaperone Trigger Factor.

2011-12-09 | E-GEOD-33671 | biostudies-arrayexpress

Direct Nucleosome Binding of Borealin Secures Chromosome Association of the Chromosomal Passenger Complex

Project description:CPC-NCP complexes were crosslinked using EDC and analysed by mass spectrometry. The results showed Borealin is critical for nucleosome binding made extensive contacts with NCPs, whereas Survivin interactions are mostly limited to the BIR domain and the H3 N-terminal tail as expected. Mapping the crosslinks onto the three dimensional structures of NCP and CPC suggests a model where the localisation module of the CPC together with a highly basic N-terminal tail of Borealin docks onto the acidic patch formed by H2A and H2B, a surface commonly involved in nucleosome recognition. This interaction may orient the Survivin BIR domain to facilitate binding of histone H3 tail phosphorylated at Thr3. Notably, Borealin loop residues trace along the DNA-histone interface implying its major contribution to nucleosome binding involves both protein-histone and possibly protein-DNA contacts.

2019-09-30 | PXD012882 | Pride

Investigating the monomer-dimer transition of PKD1 kinase domain with EDC crosslinking

Project description:The project aim was to generate experimental constraints for the in silico modeling of the dimeric structure of the PKD kinase domain. And identify conformational changes upon dimerization. For this we used the heterobifunctional zero length crosslinker EDC to identify salt bridges within the protein and between the molecules in the dimeric arrangement. We could observe a stabilization of the protein in particularly in the activation loop upon dimerization and successfully identified one abundant dimer specific crosslink that helped us to identify contact surfaces in the dimer interface.

2023-03-11 | PXD031997 | Pride

Structure of the human FERRY Rab5 effector complex

Project description: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 determine the cryo-EM structure of the human FERRY complex, composed of Fy-1 to Fy-5. The structure reveals a clamp-like architecture, in which two arm-like appendages, each consisting of Fy-2 and a Fy-5 dimer, protrude from the central Fy-4 dimer. We demonstrate that the coiled-coil domains of Fy-2 are flexible and project into opposite directions from the FERRY complex core. While the C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils together with Fy-5 bind mRNA. Thus, Fy-2 serves as binding hub that connects not only all five complex subunits, but also mediates the binding to mRNA and to the early endosome via Rab5. The FERRY structure provides novel mechanistic insight into long-distance mRNA transport.

2023-10-23 | PXD034875 | Pride

Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions

Project description:In the present paper, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. To prove this three model systems, a) a small synthetic peptide from smB'/B protein incubated with U1snRNA oligonucleotide, b) in vitro reconstituted 15.5K protein with U4 snRNA oligonucleotide and c) native ribonucleoprotein-complexes (RNPs) from S. cerevisiae were used . All protein-RNA complexes were UV irradiated and heteroconjugates cross-linked enriched prior to LC-MS analysis. Our results unambiguously show that DTT covalently participates in cysteine-uracil crosslinks which is observable as a mass increments of 152 Da upon mass spectrometric analysis.

2015-10-13 | PXD002656 | Pride

Dithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions

2022-03-01 | PXD002392 | Pride

Crosslinking mass spectrometry of the unconventional kinetoplastid kinetochore protein KKT4

Project description:The kinetochore is the macromolecular protein machine that drives chromosome segregation by interacting with spindle microtubules. Unlike most other eukaryotes that have canonical kinetochore proteins, a group of evolutionarily divergent eukaryotes called kinetoplastids (such as Trypanosoma brucei that causes human African trypanosomiasis) have a unique set of kinetochore proteins. To date, the only kinetoplastid kinetochore protein that is known to bind microtubules is KKT4, which has no high-resolution structure information available. Here we used X-ray crystallography, NMR spectroscopy, and crosslinking mass spectrometry to characterise the structure and dynamics of KKT4.

2020-10-15 | PXD020229 | Pride

Native alpha synuclein crosslinking

Project description:Alpha synuclein in it's native state in solution was crosslinked using a variety of short-range crosslinking reagents. Crosslinks detected by mass spectrometry were then used as constraints in a discrete molecular dynamics simulation of the synuclein protein, and a structural ensemble of the protein was determined.

2019-02-28 | PXD011645 | Pride

PTPN21 and Hook3 relieve KIF1C autoinhibition and activate intracellular transport

Project description:The kinesin-3 KIF1C is a fast organelle transporter implicated in the transport of dense core vesicles in neurons and the delivery of integrins to cell adhesions. Here we report the mechanisms of autoinhibition and release that control the activity of KIF1C. We show that the microtubule binding surface of KIF1C motor domain interacts with its stalk and that these autoinhibitory interactions are released upon binding of protein tyrosine phosphatase PTPN21. The FERM domain of PTPN21 stimulates dense core vesicle transport in primary hippocampal neurons and rescues integrin trafficking in KIF1C-depleted cells. In vitro, human full-length KIF1C is a processive, plus-end directed motor. Its landing rate onto microtubules increases in the presence of either PTPN21 FERM domain or the cargo adapter Hook3 that binds the same region of KIF1C tail. This autoinhibition release mechanism allows cargo-activated transport and might enable motors to participate in bidirectional cargo transport without undertaking a tug-of-war.

2019-06-24 | PXD013939 | Pride

The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities

Project description:The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor, which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution and quantitative fluorescence microscopy in live cells. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work unveils likely pathophysiologically relevant quaternary assemblies of the nuclear receptor with important implications for glucocorticoid action and drug design.

2023-03-11 | PXD028039 | Pride