Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-Linking/mass spectrometry (CLMS) analysis of RNA polymerase II

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Zhuo Chen

LAB HEAD: Juri Rappsilber

PROVIDER: PXD010481 | Pride | 2018-07-20

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	PolII_XiVersion1.6.742.csv	Csv
	PolII_XiVersion1.6.742_Links_xiFDR1.1.27.csv	Csv
	PolII_XiVersion1.6.742_PSM_xiFDR1.1.27.csv	Csv
	Rappsilber_CLMS_PolII_1.RAW	Raw
	Rappsilber_CLMS_PolII_1.mgf	Mgf

Items per page:

1 - 5 of 12

Similar Datasets

Cross-Linked/Mass-spectrometry analysis of RNA-Polimerase II

Project description:The data of a previous publication (Chen et.al. 2009 doi:10.1038/emboj.2009.401) where reprocesed and then used to validate false discovery rate calculations for unique residue pairs.

2017-03-09 | PXD004749 | Pride

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

Capturing protein communities by structural proteomics in a thermophilic eukaryote

Project description:The arrangement of proteins into complexes is a key organizational principle for many cellular functions. Although the topology of many complexes has been systematically analyzed in isolation, their molecular sociology in situ remains elusive. Here, we show that crude cellular extracts of a eukaryotic thermophile, Chaetomium thermophilum, retain basic principles of cellular organization. Using a structural proteomics approach, we simultaneously characterized the abundance, interactions and structure of a third of the C. thermophilum proteome within these extracts. We identified 27 distinct protein communities that include 108 interconnected complexes, which dynamically associate with each other and functionally benefit from being in close proximity in the cell. Furthermore, we investigated the structure of fatty acid synthase within these extracts by cryoEM and this revealed multiple, flexible states of the enzyme in adaptation to its association with other complexes, thus exemplifying the need for in situ studies. As the components of the captured protein communities are known – at both the protein and complex level – this study constitutes another step forward towards a molecular understanding ofsubcellular organization.

2017-07-26 | PXD006626 | Pride

A folded conformation of MukBEF and Cohesin

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

A folded conformation of MukBEF and Cohesin

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

Quantitative cross-linking/mass spectrometry analysis revealed unknown structure of complement iC3

Project description: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 of the complement system that is a key first line of antimicrobial defense. QCLMS revealed structural differences and similarities between iC3 and C3, as well as between iC3 and C3b that is a pivotal proteolytic cleavage product of C3 and is functionally similar to iC3. Considered in combination with the crystal structures of C3 and C3b, our data support a model wherein the thioester-containing domain of C3 swings to the other end of the molecule creating, in iC3, a stable C3b-like platform for binding the zymogen, factor B, or the regulator, factor H. The integration of available crystallographic and QCLMS data allowed the determination of a 3D model for iC3. The unique arrangement of domains in iC3, which retains the anaphylatoxin (ANA) domain (while ANA is excised when C3 is enzymatically activated to C3b), is consistent with observed differences in activation and regulation between iC3 and C3b.

2016-06-17 | PXD003486 | Pride

Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes

Project description: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 that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks.

2016-06-16 | PXD001675 | Pride

Cross-linking/mass spectrometry analysis of AUGMIN complex

Project description:We applied cross-linking/mass spectrometry to characterize in vivo Augmin from Drosophila in absence of any other structural information. The identified cross-links revealed topology of the Augmin complex and allowed us to predict potential interfaces between Augmin and γ-TuRC.

2017-04-04 | PXD006246 | Pride

A model dataset for quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers

Project description: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 using isotope-labelling for quantitation, we generated a model dataset by cross-linking human serum albumin (HSA) with the readily available cross-linker BS3-d0/d4 in different heavy/light ratios.

2016-05-06 | PXD004107 | Pride

Structure of transcribing RNA polymerase II-Elongin complex

Project description:Elongin is a hetero-trimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. We solved three structures of human Elongin bound to transcribing Pol II using cryo-EM assisted by crosslinking mass spectrometry. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-8 ELOC subunit heterodimer. ELOA contains an N-terminal ‘latch’ that binds between the end of the RPB1 bridge helix and the funnel helices, thereby inducing a conformational change near the Pol II active center. The latch is strictly required for the elongation-stimulatory activity of Elongin, but not for its binding to Pol II, indicating that Elongin functions by allosterically influencing the conformational mobility of the active center. Structural comparisons show that Elongin binding to Pol II is incompatible with association of super elongation complex, the PAF1 complex, and RTF1, which also contains a latch element that stimulates Pol II.

2023-10-11 | PXD045446 | Pride