Structural study of human MRE11-RAD50-NBS1 (MRN) complex by crosslinking mass spectrometry
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Jia-Xuan Chen
LAB HEAD: Karl-Peter Hopfner
PROVIDER: PXD067324 | Pride | 2025-08-13
REPOSITORIES: Pride
Dataset's files
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Ataxia telangiectasia mutated (ATM) is a protein that belongs to the family of phosphatidylinositol 3-kinase (PI3K)-like serine/threonine kinases. Initially identified as a nuclear protein essential for the DNA damage response (DDR) in mitotic cells, it serves as repair coordinator for DNA double-strand breaks (DSBs). Dysfunction of the ATM protein underlies ataxia telangiectasia (A-T), a rare autosomal recessive disorder characterized by immunodeficiency and progressive cerebellar degeneration leading to ataxia. The cause of cerebellar neurodegeneration cannot be explained at present, given that in postmitotic neurons ATM has a cytoplasmic localization. The non-nuclear functions of ATM and their mechanistic link to cerebellar degeneration in A-T remain elusive. In this study we established both phosphoproteomic and proteomic profiles of ATM deficiency in neuroblastoma cells and mouse cerebellum tissue to identify the underlying molecular mechanism and relevant signaling networks.
2025-09-29 | PXD058394 | Pride
Project description:The mass spectrometry data of a previous publication (Chen et.al. 2009 doi:10.1038/emboj.2009.401) were reprocesed and is used for method developing, teaching and training purpose.
2018-07-20 | PXD010481 | Pride
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
Project description:Structural maintenance of chromosomes (SMC)-kleisin complexes organize chromosomal DNAs in all domains of life, where they have key roles in chromosome segregation, DNA repair and regulation of gene expression. They function through topological entrapment and active translocation of DNA, but the underlying conformational changes are largely unclear. Using structural biology, mass spectrometry and cross-linking, we investigated the architecture of two evolutionarily distant SMC-kleisin complexes: proteobacterial MukBEF and eukaryotic cohesin. We show that both contain a dynamic coiled-coil discontinuity, the elbow, near the middle of their arms that permits a folded conformation. Bending at the elbow brings into proximity the hinge dimerization domain and the head/kleisin module, situated at opposite ends of the arms. Our findings favor SMC activity models that include a large conformational change in the arms, such as a relative movement between DNA binding sites during DNA loading and translocation
2019-03-01 | PXD012377 | Pride
Project description:PleasStructural maintenance of chromosomes (SMC)-kleisin complexes organize chromosomal DNAs in all domains of life, where they have key roles in chromosome segregation, DNA repair and regulation of gene expression. They function through topological entrapment and active translocation of DNA, but the underlying conformational changes are largely unclear. Using structural biology, mass spectrometry and cross-linking, we investigated the architecture of two evolutionarily distant SMC-kleisin complexes: proteobacterial MukBEF and eukaryotic cohesin. We show that both contain a dynamic coiled-coil discontinuity, the elbow, near the middle of their arms that permits a folded conformation. Bending at the elbow brings into proximity the hinge dimerization domain and the head/kleisin module, situated at opposite ends of the arms. Our findings favor SMC activity models that include a large conformational change in the arms, such as a relative movement between DNA binding sites during DNA loading and translocatione provide an overall description of your study, think something similar in scope to the manuscript abstract
2019-03-01 | PXD012370 | Pride
Project description:DNA Double Strand Breaks (DSBs) are harmful lesions that require rapid detection and repair in order to avoid toxic genomic rearrangements. DSBs elicit the so called DNA Damage Response (DDR), largely relying on ataxia telangiectasia mutated (ATM) and DNA Protein Kinase (DNAPK), two members of the PI3K-like kinase family, whose respective functions during the sequential steps of the DDR remains controversial. Using the DIvA cell line, expressing the AsiSI restriction enzyme, we have investigated the role of ATM and DNAPK in several aspects of the DDR upon induction of multiple clean DSBs throughout the human genome. High resolution mapping revealed that they are activated and spread in cis on a confined region surrounding all DSBs, independently of the pathway used for repair. However, a thorough analysis of repair kinetics, H2AX domain establishment and H2AX foci structure and dynamics revealed non overlapping functions for the two kinases once recruited at DSBs. Our results suggest that ATM is not solely acting on chromatin marks but also on chromatin organisation in order to ensure repair accuracy and survival.
2015-09-30 | E-MTAB-2992 | biostudies-arrayexpress
Project description:Quantitative cross-linking/mass spectrometry (QCLMS) provides increasing structural detail on altered protein states in solution. Accurate quantitation is a value in itself but may also be central to elucidating small differences between protein states. Hence, QCLMS could benefit from data independent acquisition (DIA) which generally provides higher reproducibility than data dependent acquisition (DDA) and higher throughput than targeted methods. Therefore we here open DIA to QCLMS by extending a widely used DIA software, Spectronaut to now also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 9.8%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favourably to DDA where we previously quantified only 63% of the identified cross-links across triplicates with a CV of 14%, for a single protein and complete manual data curation. DIA QCLMS is promising to detect differential abundance of cross-linked peptides in complex mixtures despite the encountered ratio compression when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.
2019-01-25 | PXD011036 | Pride
Project description:Mitochondria derived from Saccharomyces cerevisiae grown on either a non-fermentable (glycerol) or a fermentable (glucose) carbon source were cross-linked with BS3. Additionally, by using a stable-isotope labelled quantitative cross-linking approach, we were able to quantify differences in protein-protein cross-links in mitochondria according to the growth condition. Furthermore, so far uncharacterized yeast proteins were put into biological context based on their cross-linking pattern.
2020-04-27 | PXD017620 | Pride
Project description:Culex pipiens pallens and Cx. p. quinquefasciatus are important vectors of many diseases, such as West Nile fever and lymphatic filariasis. The widespread use of insecticides to control these disease vectors and other insect pests has led to insecticide resistance becoming common in these species. High throughput screening using SSH and specific microarray platforms was thought to have identified some resistance-related genes. However, limitations of these methods meant that only a few hundred of the many thousand genes could be screened. It wasn’t until the sequencing of the Cx. quinquefasciatus genome in 2010 that it became possible to screen all 18.9 thousand genes in the mosquito genome for anti-insecticidal activity. We used high throughout Illumina sequencing to identify hundreds of Cx. p. pallens and Cx. p. quinquefasciatus genes that were differentially expressed in response to pesticide exposure. The identification of these genes is a vital first step for more detailed investigation of the molecular mechanisms involved in insecticide resistance in mosquitoes. In this study, larvae of Cx. pipiens pallens and Cx. pipiens quinquefasciatus were collected from field and transported to the laboratory and reared to adulthood to get F1 generation. Then, half of the F1 generation was conducted to pesticide bioassay. RNA extraction and Illumina sequencing were undertaken in another half of the F1 generation. Therefore, Samples used in Illumina sequencing did not contact any insecticides. Twelve Cx. pipiens pallens and Cx. pipiens quinquefasciatus lavae were undertaken Illumina RNA sequencing.
2014-05-07 | E-GEOD-57307 | biostudies-arrayexpress
Project description:This project aims to elucidate a novel molecular mechanism driving mechanical allodynia, a debilitating neuropathic pain condition. We focus on a spinal cord “allodynia gate” circuit in which nerve injury leads to disinhibition of protein kinase Cγ (PKCγ) excitatory neurons. Our findings reveal that this disinhibition is mediated by endocannabinoid (eCB) signaling: eCBs released from PKCγ neurons activate presynaptic cannabinoid receptor 1 (CB1R) located on glycinergic (Gly) neurons. A key event in this process is the functional interaction between CB1R and glycine transporter 2 (GlyT2) within Gly neurons. However, the structural basis of the CB1R–GlyT2 complex remained poorly understood. The mass spectrometry data presented in this repository directly address this knowledge gap. Using chemical cross-linking mass spectrometry (CX-MS) with the BS³ cross-linker, we mapped specific interaction interfaces between the N-terminal domain of CB1R and defined extracellular and intracellular domains of GlyT2. The protein–protein interaction identified by CX-MS was independently validated by co-immunoprecipitation (Co-IP) assays. The structural insights derived from this CX-MS dataset enabled the rational design of a disrupting peptide, Tat-STVKIAK-KFERQ, which targets the CB1R–GlyT2 interface. This peptide effectively prevented and alleviated nerve injury–induced mechanical allodynia in mice. Thus, the data provided here not only provide critical structural evidence for a pivotal protein complex in neuropathic pain but also establish a foundation for a targeted therapeutic strategy.
2026-02-13 | PXD070478 | Pride