Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A2M-3K DSSO cross-linking to identify the bait region position

ABSTRACT: An A2M mutant, A2M-3K, with the bait region arginines replaced with lysines, was cross-linked with DSSO. Its monomeric gel band was analyzed by XL-MS to identify the bait region position within a subunit.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Seandean Harwood

LAB HEAD: Jan J. Enghild

PROVIDER: PXD019048 | Pride | 2021-05-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20200115_A2M_OG3K_ingel_GluC_monomer_1.raw	Raw
	20200115_A2M_OG3K_ingel_GluC_monomer_2.raw	Raw
	20200115_A2M_OG3K_ingel_GluC_monomer_3.raw	Raw
	20200115_A2M_OG3K_ingel_GluC_monomer_4.raw	Raw
	20200115_A2M_OG3K_ingel_GluC_monomer_5.raw	Raw

Items per page:

1 - 5 of 19

Similar Datasets

CX-MS of DSSO-cross-linked A2M - Structural investigations of human α2-macroglobulin elucidate its native conformation and inhibitory mechanism

Project description:Human A2M was cross-linked with DSSO in its native, methylamine-treated, and trypsin-cleaved conformations. The monomer, dimer, and tetramer SDS-PAGE gel bands of native A2M were analyzed by in-gel digest. Total protein digests of all three conformations were analyzed and compared.

2021-05-21 | PXD019101 | Pride

A2M bait region engineering - autoconjugation product cross-link identification and PRM quantification

Project description:In-gel digest of a cross-linked product band was used to identify an internal isopeptide cross-link formed in A2M TR K704 upon bait region cleavage by trypsin. PRM was used to quantify the thiol ester in native PAGE bands of A2M nEXT and EXT mutants.

2021-09-10 | PXD023651 | Pride

The structures of R124H and R555W TGFBIp suggest a direct role of the mutated residues in the aggregation of TGFBIp in granular corneal dystrophy

Project description:Protein aggregation in the outermost layers of the cornea, leading to cloudy vision and in severe cases blindness, is linked to mutations in the extracellular matrix protein, transforming growth factor-β-induced protein (TGFBIp). Among the most frequent disease-causing mutations are R124H and R555W, both associated with granular corneal dystrophy (GCD) characterized by early-onset amorphous aggregation. The molecular mechanisms of protein aggregation in GCD are largely unknown. In this study, we determined the crystal structures of R124H and R555W. Whereas no structural changes of mutated monomeric TGFBIp can explain its aggregation propensity, the two mutations facilitate a new dimer interface in the crystal packing, not appearing in the wild-type structure. The interface in both R124H and R555W structures are centered on residue 124 in one TGFBIp molecule and 555 in a second TGFBIp molecule. This unique interface of R124H and R555W is not compatible with arginines at positions 124 and 555 as seen in wild-type TGFBIp. Hence, this intermolecular interaction may underlie the similar aggregation behavior exhibited by the two TGFBIp mutants in vivo. Using cross-linking mass spectrometry, we identified and characterized a dimer of TGFBIp wild-type and mutants in solution. The soluble dimers also involve interactions between the N- and C-terminal domains of two TGFBIp molecules but is not identical to the crystal packing dimer interface involving R124H and R555W. Targeting of the crystal packing dimer interface might offer new opportunities for therapeutic intervention to treat patients with GCD.

2021-09-08 | PXD022976 | Pride

Biochemically validated structural model of the 15-subunit intraflagellar transport complex IFT-B

Project description:Cilia are ubiquitous eukaryotic organelles impotant for cellular motility, signaling, and sensory reception. Cilium formation requires intraflagellar transport of structural and signaling components and involves 22 different proteins organized into intraflagellar transport (IFT) complexes IFT-A and IFT-B that are transported by molecular motors. The IFT-B complex constitutes the backbone of polymeric IFT trains carrying cargo between the cilium and the cell body. Currently, high-resolution structures are only available for smaller IFT-B subcomplexes leaving > 50% structurally uncharacterized. Here, we used Alphafold to structurally model the 15-subunit IFT-B complex. The model was validated using cross-linking/mass-spectrometry data on reconstituted IFT-B complexes, X-ray scattering in solution, diffraction from crystals as well as site-directed mutagenesis and protein-binding assays. The IFT-B structure reveals an elongated and highly flexible complex consistent with cryo-electron tomographic reconstructions of IFT trains. The IFT-B complex organizes into IFT-B1 and IFT-B2 parts with binding sites for ciliary cargo and the inactive IFT dynein motor, respectively. Interestingly, our results are consistent with two different binding sites for IFT81/74 on IFT88/70/52/46 suggesting the possibility of different structural architectures for the IFT-B1 complex. Our data present a structural framework to understand IFT-B complex assembly, function, and ciliopathy variants.

2022-12-02 | PXD037049 | Pride

Reconstitution of mammalian Cleavage Factor II

Project description:Cleavage factor II (CF II) is a poorly characterized component of the multi-protein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage. CF II binds RNA with nanomolar affinity. Binding is mediated mostly by the two zinc fingers in the C-terminal region of hPcf11. RNA is bound without pronounced sequence-specificity, but extended G-rich sequences appear to be preferred. We discuss the possibility that CF II contributes to the recognition of cleavage/polyadenylation substrates through interaction with G-rich far-downstream sequence elements.

2020-05-26 | PXD010177 | Pride

Structural Analysis of 70S Ribosomes by Cross-Linking/Mass Spectrometry Reveals Conformational Plasticity

Project description:We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-link-pairs and 3,405 intermolecular distances for 97 protein pairs. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS.

2020-08-13 | PXD018935 | Pride

Identification and Expression Patterns of Novel Long Non-Coding RNAs in Neural Progenitors of the Developing Mammalian Cortex

Project description:Long non-coding (lnc)RNAs play key roles in many biological processes. Elucidating the function of lncRNAs in cell type specification during organ development requires knowledge about their expression in individual progenitor types rather than in whole tissues. To achieve this during cortical development, we used a dual-reporter mouse line to isolate coexisting proliferating neural stem cells, differentiating neurogenic progenitors and newborn neurons and assessed the expression of lncRNAs by paired-end, high-throughput sequencing. We identified 379 genomic loci encoding novel lncRNAs and performed a comprehensive assessment of cell-specific expression patterns for all, annotated and novel, lncRNAs described to date. Our study provides a powerful new resource for studying these elusive transcripts during stem cell commitment and neurogenesis. mRNA profiles of Proliferating Progenitors, Differentiating Progenitors and Neurons from lateral cortex of E14.5 mouse embryos. Each cell type in three biological replicates.

2015-04-23 | E-GEOD-65487 | biostudies-arrayexpress

Cross-linking of mouse laminin 111

Project description:Laminin, a ~800 kD heterotrimeric protein, is a major functional component of the extracellular matrix, contributing to tissue development and maintenance. We used cross-linking and mass spectrometry to determine the order of subunits in the ~750 Å trimeric coiled-coil oligomerization domain of laminin and to achieve an estimate of the register of the three subunits along the length of the coiled coil.

2016-12-22 | PXD004898 | Pride

A2M Q975C and C3 Q1013C disulfide mutants

Project description:Mutant A2M and C3 with disulfides replacing their thiol esters were disulfide mapped via pepsin digests.

2021-02-18 | PXD019082 | Pride

Cross-linking mass spectrometry and integrative modelling of Methanocaldococcus jannaschii GMP synthetase

Project description:GMP synthetases are enzymes that catalyze the conversion of XMP to GMP. The two-subunit type GMP synthetases are composed of a glutamine amidotransferase (GATase) subunit that catalyzes the conversion of Gln to Glu and ammonia, and the ATP pyrophosphatase (ATPPase) subunit that catalyzes the formation of AMP-XMP from ATP and XMP. The inactive GATase subunit is allosterically activated by the binding of substrates to the ATPPase subunit. Upon activation, the GATase subunit binds Gln and hydrolyzes it producing ammonia which is tunnelled to the ATPPase subunit. The two subunits form a tight complex to enable domain crosstalk. However, the Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is unique as the GATase (MjGATase) and ATPPase (MjATPPase) subunits interact transiently. Here, we employed enzyme kinetics, X-ray crystallography, cross-linking mass spectrometry (XL-MS) and integrative modelling to understand the mechanistic basis for the various steps in the catalytic cycle of MjGMPS.

2022-09-02 | PXD031519 | 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