Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spirochaeta africana RNAP holoenzyme

ABSTRACT: Crosslinking mass spectrometry was applied to investigate the localization of ÏƒR1.1 domain in the structure of Spirochaeta africana RNA polymerase holoenzyme. RNA polymerase holoenzymes were assembled using polymerase core subunits and Ïƒ factor heterologously expressed in Escherichia coli. Two complexes were assembled in the absence of S. africana CarD activator and two in the presence of CarD activator. The resulting four complexes were crosslinked using disuccinimidyl sulfoxide (DSSO). Crosslinked protein complexes were analyzed by LC-MS/MS, and crosslinked residue pairs were identified in the form of crosslinked peptides.

ORGANISM(S): Spirochaeta Africana

SUBMITTER: Georgiy A. Belogurov

PROVIDER: PXD074046 | JPOST Repository | Fri May 01 00:00:00 BST 2026

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	250217_sfc_holo_MS2_MS2_MS3_1500ng.csv	Csv
	250217_sfc_holo_MS2_MS2_MS3_1500ng.fasta	Fasta
	250217_sfc_holo_MS2_MS2_MS3_1500ng.raw	Raw
	250217_sfc_holo_card__MS2_MS2_MS3_1500ng.csv	Csv
	250217_sfc_holo_card__MS2_MS2_MS3_1500ng.fasta	Fasta

Items per page:

1 - 5 of 12

Similar Datasets

Crosslinking/mass spectrometry analysis of Bacillus subtilis RNAP-Delta-HelD complexes

Project description:Crosslinking mass spectrometry was applied to investigate protein contacts and dramatic structural rearrangements triggered by HelD binding to RNAP. Four complexes RNAPΔδΔHelD , RNAPΔδΔHelD-δ, RNAPΔδΔHelD-HelD and RNAPΔδΔHelD-δ-HelD were assembled using RNAP purified from B. subtilis ΔhelDΔropE strain (RNAPΔδΔHelD), and recombinant δ and HelD. The four complexes were crosslinked using a heterobifunctional, photoactivatable crosslinker sulfosuccinimidyl 4,4′‐azipentanoate (sulfo-SDA). Crosslinked protein complexes were analyzed by LC-MS/MS, and crosslinked residue pairs were identified in form of crosslinked peptides.

2020-10-26 | PXD019437 | JPOST Repository

Structure of Saccharomyces cerevisiae Mediator-RNA polymerase II pre-initiation complex for divergent transcription

Project description:This study has determined structure of transcription initiation complexes including a DNA-bound activator, RNA polymerase II (Pol II), and Mediator on a divergent promoter GAL80/SUT719 using a combination of cryo-EM and XL-MS analyses. Our cryo-EM single-particle analysis reveals a dimeric form of Med-PIC through the Mediator Tail module induced by the activator protein. Density of the upstream DNA bound to the Gal4-VP16 was identifiable along the Mediator Tail module, while XL-MS localized flexible regions that were not visible by cryo-EM analysis, such as activator-binding domains (ABDs and KIX).

2024-05-22 | PXD036149 | Pride

ChIP-seq of the multiple antibiotic resistance activator (MarA) protein and RNA polymerase sigma70 subunit of Enterotoxigenic Escherichia coli strain H10407

Project description:The experiment contains ChIP-seq data for Enterotoxigenic Escherichia coli strain H10407 transformed with plasmid pRGM9818. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using antibodies against MarA, MarR or the RNA polymerase sigma 70 subunit. Libraries were prepared using DNA remaining after immunoprecipitation. Note that the MarR immunoprecipitations were not successful but the data served as a useful control for non-specifically immunoprecipitated DNA sequences.

2017-09-30 | E-MTAB-5521 | biostudies-arrayexpress

Structural basis of the SWI/SNF-bound transcription pre-initiation complex

Project description:DSSO crosslinking of SwiSnf + Mediator + Pre-initiation Complex. Two replicate experiments starting with 300 ug of protein and 6 mM DSSO. Crosslinked peptides were fractionated by size-exclusion chromatography (SEC) and 8 SEC were analyzed by LC-MS on an Orbitrap Exploris 480 instrument. The first set of 8 fractions was run in technical replicate, once with a FAIMS source and once without.

2025-05-14 | MSV000097892 | MassIVE

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP: sequencing data

Project description:We applied 4-thiouridine to cultured cells expressing the FLAG/HA-tagged RNA-binding proteins (RBPs) followed by UV 365 nm irradiation. The crosslinked RNA-protein complexes were isolated by immunoprecipitation, and the covalently bound RNA was partially digested with RNase T1 and radiolabeled. The radiolabeled RNPs were subsequenctly separated by SDS-PAGE, the crosslinked RNA segments recovered and converted into a cDNA library and sequenced.

2010-05-21 | GSE21918 | GEO

Systematic Discovery of Deeply Conserved Plant Protein Complexes, Chlamydomonas reinhardtii, DSSO crosslinking

Project description:The associated files are mass spec data from size exclusion chromatography fractions that were subsequently crosslinked with DSSO and digested with one of two enzymes, Trypsin or Chymotrypsin. The starting material was a native extract prepared from Chlamydomonas reinhardtii. The mass spectrometry used a data-dependent MS2-MS3 method to identify crosslinks.

2019-10-28 | PXD013735 | Pride

An UBX domain in UBXD1 organizes Ub binding at the C-terminus of the VCP/p97 AAA-ATPase

Project description:Identification of crosslinked peptides between UBXD1 and HR23b using different cross-linking approaches (chemical cross-linking with DSSO and photo crosslinking with incorporated BPA).

2023-05-25 | PXD040984 | Pride

An UBX domain in UBXD1 organizes Ub binding at the C-terminus of the VCP/p97 AAA-ATPase

Project description:Identification of crosslinked peptides between UBXD1, Ubiquitin and p97 using different cross-linking approaches (chemical cross-linking with DSSO, photo crosslinking with incorporated BPA or photo-Met)

2023-05-25 | PXD039606 | Pride

Reanalysis of a synthetic cross-linked peptide library with MaxLynx

Project description:Reanalysis of a synthetic crosslinked peptide library datasets with DSS (non-cleavable), DSSO and DSBU (MS-cleavable) cross linkers from Beveridge et al., Nat. Commun., 2020 (PXD014337)

2022-01-11 | PXD027159 | Pride

Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor that promotes stress recovery

Project description:We develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes (APEX-PS).

2021-03-18 | MSV000087070 | MassIVE