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ProteomicsA model dataset for quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers
Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue-resolution data on static proteinaceous structures. In order to investigate the technical feasibility of recording dynamic processes u...
ORGANISM(S): Homo sapiens (Human) 
2016-05-06 | PXD004107 | Pride
Model dataset Isotope-labeled cross-linkers Hsa Quantitative cross-linking/mass spectromentry 
ProteomicsQuantitative cross-linking/mass spectrometry reveals subtle protein conformational changes
We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-06-16 | MSV000079827 | MassIVE
ProteomicsInterrogating the interaction of fission yeast RNA-binding protein Puf3 with the Ccr4-Not complex using crosslinking mass spectrometry
mRNA decay is a key determinant of gene regulation, initiated by the shortening of mRNA poly(A) tails by the CCR4-NOT deadenylation complex. Specificity is achieved through RNA adaptors—RNA-binding proteins that recruit CCR4-NOT to specific substrate mRNAs in a regulated manner. However, the molecul...
ORGANISM(S): Schizosaccharomyces pombe 927 
2025-09-03 | PXD055147 | Pride
Crosslinking ms Idr Protein-protein interaction Rna binding protein puf3 Ccr4-not complex 
ProteomicsQuantitative cross-linking/mass spectrometry reveals subtle protein conformational changes
We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found ...
ORGANISM(S): Homo sapiens (Human) 
2016-06-16 | PXD001675 | Pride
Quantitative cross-linking/mass spectrometry  conformation changes  human c3  activation of complement system 
ProteomicsQuantitative cross-linking/mass spectrometry analysis revealed unknown structure of complement iC3
We applied quantitative cross-linking/mass spectrometry (QCLMS) to interrogate the structure of iC3 (or C3(H2O)), the activated hydrolytic product of the abundant human complement protein C3. The slow but spontaneous and ubiquitous formation of iC3 from C3 initiates antibody-independent activation o...
ORGANISM(S): Homo sapiens (Human) 
2016-06-17 | PXD003486 | Pride
Quantitative cross-linking/mass spectrometry  domain architecture  activation of complement system  alternative pathway 
ProteomicsCrosslinking mass spectrometry (CLMS) analysis of monoubiquitinated FANCD2-FANCI complex
Vertebrate DNA crosslink repair excises toxic replication-blocking DNA crosslinks. Numerous factors involved in crosslink repair have been identified, and mutations in their corresponding genes cause Fanconi anemia (FA). A key step in crosslink repair is monoubiquitination of the FANCD2-FANCI hetero...
ORGANISM(S): Gallus gallus (Chicken) 
2020-03-09 | PXD017020 | Pride
Crosslinking mass spectrometry Fancd2-fanci comple Monoubiquitination Fanconi anemia pathway 
ProteomicsCrosslinking/mass spectrometry (CLMS) analysis of Cohesin complex
The ring-shaped cohesin complex is thought to fulfil its roles in sister chromatid cohesion, genome stability and gene regulation by topologically encircling DNAs. The ring is formed by two Structural Maintenance of Chromosome (SMC) subunits, whose ATPase heads are linked by a kleisin subunit. Addit...
ORGANISM(S): Schizosaccharomyces pombe 972h- 
2020-08-04 | PXD018608 | Pride
Crosslinking/mass spectrometry Cohesin complex 
ProteomicsPre-40S ribosome biogenesis factor Tsr1 is an inactive structural mimic of translational GTPases
Budding yeast Tsr1 is an essential ribosome biogenesis factor that is required for cytoplasmic steps in 40S subunit maturation. S. cerevisiae Tsr1 was expressed as an N-terminal GST fusion protein in E. coli. A mutant Tsr1ΔNΔloop was generated in which residues 410 to 476 of Tsr1 were replaced with ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-02-08 | PXD004074 | Pride
Pre-40s ribosome biogenesis Protein structure Cross-linking/mass spectrometry 
ProteomicsCrosslinking MS analysis of MCM2-7 DH-Sld3/7 complex
interrogate the 3D organization of the MCM2-7 DH-Sld3/7 complex espetically the flexible Sld3/7 regions, the MCM2-7 DH-Sld3/7 complex was analyzed by crosslinking MS
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2026-06-29 | PXD070193 | Pride
Crosslinking ms 
Proteomics3D topology of the SMC2/SMC4 sub-complex from chicken condensin I revealed by cross-linking and molecular modelling
SMC proteins are essential components of three protein complexes that are important for chromosome structure and function. The cohesin complex holds replicated sister chromatids together, whereas the condensin complex has an essential role in mitotic chromosome architecture. Both are involved in int...
ORGANISM(S): Gallus gallus (Chicken) 
2015-07-13 | PXD001835 | Pride
Condensin Cross-linking Mass spectrometry Smc Structure Coiled-coil 
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