Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-Link of inactive PhK and GP

ABSTRACT: Phosphorylase kinase (PhK) phosphorylates GP to initiate glycogenolysis. To gain insights into the mechanism of PhK catalyzing GP phosphorylation, we have tried a variety of methods to obtain the hPhK-GP complex, but none of them were successful. Eventually, we decided to employ XL-MS to investigate the interaction between PhK and GP.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Suspension Culture

SUBMITTER: Ruifang Ma

LAB HEAD: Kaige Yan

PROVIDER: PXD059356 | Pride | 2025-05-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	checksum.txt	Txt
	inactive1_1.raw	Raw
	inactive1_2.raw	Raw
	inactive1_3.raw	Raw
	inactive2_1.raw	Raw

Items per page:

1 - 5 of 9

Publications

Molecular basis for the regulation of human phosphorylase kinase by phosphorylation and Ca<sup>2</sup>.

Ma Ruifang R Du Bowen B Shi Chen C Wang Lei L Zeng Fuxing F Han Jie J Guan Huiyi H Wang Yong Y Yan Kaige K

Nature communications 20250328 1

Phosphorylase kinase (PhK) regulates the degradation of glycogen by integrating diverse signals, providing energy to the organism. Dysfunctional mutations may directly lead to Glycogen Storage Disease type IX (GSD IX), whereas the abnormal expression of PhK is also associated with tumors. Here, we use cryo-electron microscopy (cryo-EM) to resolve its near-atomic structures in the inactive and active states. These structures reveal the interactions and relative locations of the four subunits (αβγ ...[more]

PMID: 40148320

Similar Datasets

Cross-Link of active PhK and GP

Project description:Phosphorylase kinase (PhK) phosphorylates GP to initiate glycogenolysis. To gain insights into the mechanism of PhK catalyzing GP phosphorylation, we have tried a variety of methods to obtain the hPhK-GP complex, but none of them were successful. Eventually, we decided to employ XL-MS to investigate the interaction between active PhK and GP.

2025-05-07 | PXD059369 | Pride

Confirmation of the binding site of spermine to ATP13A2 protein

Project description:To better understand human ATP13A2-mediated polyamine transport, we used single-particle cryo-electron microscopy to solve high-resolution structures of human ATP13A2. Interestingly, we found polyamine binding at multiple sites distributed along the transmembrane regions in ATP13A2 protein, which has not been reported in previous studies. Therefore, we used cross-linking mass spectrometry (CX-MS) to confirm potential binding sites.

2023-05-10 | PXD037493 | Pride

An integrated workflow for cross-linking/mass spectrometry

Project description:We present a concise workflow to enhance the mass spectrometric detection of cross-linked peptides by introducing sequential digestion and the database search software Xi. We use sequential digestion to reduce the peptide size and increase identification rates. The methodology is independent of samples complexity, cross-linker choice, method acquisition and can be used with multiple digestion steps.

2019-08-27 | PXD008550 | Pride

Gene expression profile of mock and FLT3-ITD-expressing K562 cells.

Project description:We used whole genome microarray expression profiling as a discovery platform to identify genes regulated by FLT3-ITD activity. Viral particles with pMY-puro, pMY-puro-FLT3-ITD-1 or pMY-puro-FLT3-ITD-2, were generated using PLAT-gp packaging cells and infected to K562 cells. The vector-transduced cells were selected with 2µg/ml puromycin treatment.

2015-09-09 | E-GEOD-64330 | biostudies-arrayexpress

Structure of the Fanconi anaemia monoubiquitin ligase complex

Project description:The Fanconi Anemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks. Genetic inactivation of this pathway impairs development, prevents blood production and promotes cancer. The key molecular step in the FA pathway is the monoubiquitination of a heterodimer of FANCI-FANCD2 by the FA core complex - a megadalton multiprotein E3 ubiquitin ligase. Monoubiquitinated FANCI-FANCD2 then activates a pathway to remove the DNA crosslink. Lack of molecular insight into the FA core complex limits a detailed explanation of how this vital DNA repair pathway functions. Here we reconstituted an active, recombinant FA core complex, and used electron cryo-microscopy (cryo-EM) and mass spectrometry to determine its overall structure. The FA core complex is comprised of a central symmetric dimer of the FANCB and FAAP100 subunits, flanked by two copies of the RING finger protein, FANCL. This acts as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. The two FANCL subunits are positioned at opposite ends of the complex in an unusual asymmetric arrangement, distinct from other E3 ligases. We propose that each of the two FANCL subunits play unique roles within the complex – one is a structural component while the other monoubiquitinates FANCD2. The cryo-EM structure of the FA core complex, supported by crosslinking mass spectrometry and native mass spectrometry, therefore provides a foundation for a detailed understanding of this fundamental DNA repair pathway.

2019-10-16 | PXD014282 | Pride

Hsp multichaperone complex buffers pathologically modified Tau

Project description:Alzheimer's disease is a neurodegenerative disorder in which misfolding and aggregation of pathologically modified Tau is critical for neuronal dysfunction and degeneration. The two central chaperones Hsp70 and Hsp90 coordinate protein homeostasis, but the nature of the interaction of Tau with the Hsp70/Hsp90 machinery has remained enigmatic. Here we show that Tau is a high-affinity substrate of the human Hsp70/Hsp90 machinery forming a 710 kDa client-loading complex. Complex formation involves extensive intermolecular contacts, blocks Tau aggregation and depends on Tau’s aggregation-prone repeat region. The Hsp90 co-chaperone p23 directly binds Tau and stabilizes the multichaperone/substrate complex, whereas the E3 ubiquitin-protein ligase CHIP efficiently disassembles the machinery targeting Tau to proteasomal degradation. Because phosphorylated Tau binds the Hsp70/Hsp90 machinery but is not recognized by Hsp90 alone, the data establish the Hsp70/Hsp90 multichaperone complex as a critical regulator of Tau in neurodegenerative disorders.

2022-08-11 | PXD032037 | Pride

Effect of NaCl concentration on the transcriptional network of E. coli in glucose minimal medium with glycine betaine

Project description:The growth rate of E. coli decrease continuously with NaCl concentration, however the pattern for metabolic efficiency as measured by optical density is corralated to a change in pattern in transcription data and proteomics.The analysis of the data suggest that between 4.5 and 5% NaCl, the metabolism switched from aerobic to fermentative pathways. The response to osmotic stress is similar to a response to oxidative stress. An example how a stagewise metabolic answer may be the result of continuously increasing stress. Study of the pattern of gene expression as a function of NaCl concentrations (2%, 3.5% -2 replicates-, 4.5%, 5%, 5.5%). To compare the different conditions, cDNA was normalised to genomic DNA, gDNA.

2014-05-26 | E-GEOD-54512 | biostudies-arrayexpress

Cross-linking/mass spectrometry analysis of the AOC complex

Project description:As a part of a study on how kinetochors are assembled at the centromeres of the chromosomes, cross-linking/mass spectrometry has been applied to investigate interactions between Okp1/ Ame1 heterodimer, which is part of the COMA complex, and CENP-A from Saccharomyces cerevisiae.

2018-10-30 | PXD009648 | Pride

Complementary omics strategies to dissect p53 signaling networks under nutrient stress

Project description:Signaling trough cytoplasmic or nuclear action of p53 is a major response mechanism to cellular stresses. While p53 protein levels have been shown to increase upon nutrient stresses such as starvation, the exact signaling cascade in this context remains elusive. Here, we show in a human hepatoma cell line that nutrient withdrawal leads to robust nuclear p53 stabilization and utilize various complementary omics approaches to dissect upstream and downstream networks in the response to starvation. Using the affinity purification mass spectrometry (MS) method BioID, we determine the cytoplasmic p53 interaction network within the immediate-early starvation response and show that p53 is dissociated from several metabolic enzymes and the kinase PAK2. Direct binding of p53 DNA-binding domain and N-terminal PAK2 was confirmed with nuclear magnetic resonance (NMR) interaction studies. Furthermore, rapid immunoprecipitation MS of endogenous proteins (RIME) uncovered the nuclear interactome under prolonged starvation, where we confirmed the novel p53 interactors SORBS1, involved in insulin signaling, and UGP2, a key enzyme of glycogen synthesis. Finally, transcriptomics after p53 re-expression on a CRISPR/Cas9 knock out background revealed a distinct starvation-specific transcriptome response and suggested novel nutrient-dependent p53 target genes. Together, our complementary approaches delineate several nodes of the p53 signaling cascade in response to starvation, shedding new light on the mechanisms of p53 as a nutrient stress sensor and regulator of specific transcriptional output. Given the central role of p53 in cancer biology and the beneficial effects of fasting in cancer treatment, the identified interaction partners and networks could pinpoint novel pharmacologic targets to fine-tune p53 activity.

2022-06-09 | PXD028341 | Pride

Structural Analysis of a Prokaryotic Ribosome Using a Novel Amidinating Cross-Linker and Mass Spectrometry

Project description:The structure of the Escherichia coli ribosome, a 2.5 MDa ribonucleoprotein complex containing more than 50 proteins, was probed using the novel amidinating cross-linker diethyl suberthioimidate (DEST) and mass spectrometry. Peptide cross-links derived from this complex structure were identified at high confidence (FDR 0.8%) from precursor mass measurements and collision-induced dissociation (CID) fragmentation spectra. The acquired cross-linking data were found to be in excellent agreement with the crystal structure of the E. coli ribosome. DEST cross-links are particularly amenable to strong cation exchange (SCX) chromatography, facilitating a large-scale analysis. SCX enrichment and fractionation were shown to increase the number of cross-link spectra matches in our analysis 10-fold. Evidence is presented that these techniques can be used to study complex interactomes.

2015-12-23 | PXD003381 | Pride