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ProteomicsNse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding
Eukaryotic cells employ three SMC complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo-complex....
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-07-02 | PXD024160 | Pride
Atpase Condensin Loop extrusion Chromosome segregation Xl-ms Smc5 Smc Smc6 Genome maintenance Cohesin 
ProteomicsCalcium tunes snail mucus-based materials to multiple functions
Mucus is usually associated with a viscous fluid; yet, snails routinely manufacture various astonishing mucus-based materials with properties requiring a much higher cohesion. Snail mucus materials are tailored to different and even antagonistic functions - including lubrication, adhesion, protectio...
ORGANISM(S): Cepaea nemoralis 
2026-09-26 | PXD065814 | Pride
Hierarchical structure Calcium Collagen vi Tunable Multiple functions Mucus 
ProteomicsThe immune response against cancer is modulated by stromal cell fibronectin
The data set compares murine bone marrow stromal cells that express osterix-cre (and hence cells in which the osterix promoter is active) to the cells isolated from the same animals that did not express osterix-cre (and hence do not activate the osterix promoter). To sort these cells, we used the r...
ORGANISM(S): Mus musculus (Mouse) 
2025-06-20 | PXD065221 | Pride
Breast cancer Stromal cell Tumor microenvironment Tdtomato Bone marrow Neutrophil Osterix Ly6g Fibronectin Melanoma Myeloid Bone marrow. Extracellular matrix Murine additional keywords: immune response 
ProteomicsCryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation
Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced degradation of fructose-1,6-bisphosphatase (Fbp1) and other gluconeogenic enzymes. “GID” is a collection of...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-05-29 | PXD028579 | Pride
Gid E3 ligase complex Crzoem 
ProteomicsProtein content and proximity map of yeast nuclear mRNPs
We isolated nuclear mRNPs from yeast using an endogenous bi-molecular tagging approach on Sub2 and Hpr1.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-07-25 | PXD040736 | Pride
Cross-linking mass spectrometry (xl-ms) Mrna synthesis Mrnp assembly Rna annealing Ribonucleoprotein particles 
ProteomicsPhosphoproteomic dataset comparing wild type, bob1-1 and bob1-1dbf4∆ cells in M-phase arrested S.cerevisiae.
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, repair pathway choice – the cellular decision making underlying DSB repair – occurs at the level of DSB resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (C...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2024-02-15 | PXD042607 | Pride
Ddk Dbf4-cdc7 Cell-cycle Saccharomyces cerevisiae 
ProteomicsThe EMC acts as a chaperone to labile transmembrane domains
Structure formation of membrane proteins is error-prone and thus requires chaperones that oversee this essential process in cell biology. The ER membrane protein complex (EMC) is well-defined as a transmembrane domain (TMD) integrase. In this study, we characterize an additional chaperone function o...
ORGANISM(S): Homo sapiens (Human) 
2025-08-25 | PXD059792 | Pride
Membrane proteins Endoplasmic reticulum Chaperone Protein folding 
ProteomicsGCN2 Restrains ZAKα-Dependent TNFα Production in LPS+IFNγ Stimulated Macrophages
Macrophages orchestrate inflammation through rapid and extensive proteome remodeling, yet the translational programs governing macrophage activation remain poorly defined. Here, we show that inflammatory M(LPS+IFNγ) and reparative M(IL-4) macrophages engage fundamentally distinct translational traje...
ORGANISM(S): Mus musculus (Mouse) 
2026-09-28 | PXD075112 | Pride
Macrophage Zakα Translation Gcn2 Inflammation 
ProteomicsCullin-RING ligases target substrates with geometrically optimized catalytic partners
Cullin-RING ubiquitin ligases (CRLs) control the degradation of a wide landscape of human proteins in combination with ubiquitin-carrying enzymes (UCEs). CRL expansion during evolution is apparent, with a few dozen in yeast that function with a single UCE and as many as 300 in humans that function w...
ORGANISM(S): Homo sapiens (Human) 
2024-05-22 | PXD043523 | Pride
Ubiquitylation Cullin-ring ligase 
ProteomicsProteomics analysis of zebrafish spinal cord regeneration
Label-free mass spectrometry-based quantitative proteomics was applied to a larval zebrafish spinal cord injury model, which allows axon regeneration and functional recovery within two days (days post lesion; dpl) after a spinal cord transection in 3 day-old larvae (dpf). Proteomic profiling of the ...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2023-09-06 | PXD037590 | Pride
Regeneration Zebrafish Spinal cord Lc-ms/ms 
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