Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A hybrid structural determination approach to investigate protein-RNA complexes of the nucleocapsid protein of SARS-CoV-2

ABSTRACT: UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify the interaction sites between the N-terminal (NTD) or C-terminal domain (CTD) of the SARS-CoV-2 nucleocapsid protein and the s2m element of the viral RNA.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

DISEASE(S): Severe Acute Respiratory Syndrome

SUBMITTER: Alexander Leitner

LAB HEAD: Alexander Leitner

PROVIDER: PXD037438 | Pride | 2023-03-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	210226_LU02_mbikaki_NCTD_09.raw	Raw
	210226_LU02_mbikaki_NCTD_10.raw	Raw
	210311_LU02_mbikaki_NCTD_10.raw	Raw
	210311_LU02_mbikaki_NCTD_11.raw	Raw
	210311_LU02_mbikaki_NCTD_12.raw	Raw

Items per page:

1 - 5 of 16

Similar Datasets

Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF

Project description:UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify RNA-binding regions of enhancer RNAs (eRNAs) to the negative elongation factor (NELF) complex, and NELF as part of the paused elongation complex (PEC) of human RNA polymerase II.

2022-03-08 | PXD030569 | Pride

Structural insights into protein-RNA interactions within biomolecular condensates using UV cross-linking and mass spectrometry

Project description:UV-light-induced protein-RNA cross-linking followed by MS analysis was used to identify the interaction sites between protein and RNA in different phase-separated and non-phase separated states of complexes involving the following proteins: PTBP1, FUS, and SARS-CoV-2 nucleocapsid protein.

2024-03-06 | PXD046267 | Pride

Sensitive detection and structural characterisation of UV-induced cross-links in protein-ribonucleic acid complexes using stable isotope labelling and mass spectrometry

Project description:The recently introduced cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) technique enables protein-RNA cross-links to be used as precisely localized distance restraints in de novo structural modelling, but little is known about the structural characteristics of UV-induced cross-links. Here we demonstrate protocol optimizations, and apply the enhanced protocol to a set of model protein-RNA complexes to better characterize the properties of UV-induced protein-RNA cross-links. We use these insights to study a non-canonical protein-RNA interaction between SF3A1 of the U2 snRNP and stem-loop 4 of the U1 snRNP, demonstrating that UV cross-linking and mass spectrometry is a reliable standalone data type for low resolution structural characterizations of protein-RNA interactions.

2023-09-06 | PXD029930 | Pride

Sequence specific recognition of U1 snRNP stem-loop 4 by the ubiquitin-like domain of U2 snRNP protein SF3A1 and its RGG motif

Project description:Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the ubiquitin-like domain (UBL) of the protein SF3A1, a component of the U2 snRNP, with stem-loop 4 RNA (SL4) from the U1 snRNP. The complex was cross-linked and analysed both in isolation, and in broader context with components of the U1 snRNP. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.

2022-02-22 | PXD027189 | Pride

RNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data

2023-09-06 | PXD039754 | Pride

Hybrid structural modeling of protein-RNA complexes using crosslinking of segmentally isotope labeled RNA and tandem mass spectrometry

Project description:To study protein-RNA interactions at single amino acid and single nucleotide resolution we developed a new approach, termed cross-linking of segmentally isotope labeled RNA and tandem mass spectrometry (CLIR-MS/MS). The method was developed using the PTBP1-EMCV IRES complex as a model system and additionally applied to the U1 snRNP complex. Data from both complexes are included in this submission.

2017-03-27 | PXD005566 | Pride

Integrative structure determination of an 85-kilodalton PTBP1-IRES complex in solution reveals a strong compaction with pronounced conformational flexibility

Project description:Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the interaction between the four RNA recognition motifs (RRMs) of the protein PTBP1 with the internal ribosome entry site (IRES) of encephalomyocarditis virus (EMCV). These results are a reanalysis of PXD005566, with a broader parameter set.

2023-10-24 | PXD034894 | Pride

Structural requirements for photo-induced RNA-protein cross-linking

Project description:Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the UV cross-linking behavior of in vitro reconstituted FOX1 RRM in complex with its cognate RNA sequence, the Fox binding element (FBE), (U)GCAUGU. The FBE heptanucleotide was subsequently mutated, and the impact on UV cross-linking and affinity investigated. Cross-linking was performed using irradiation under 254 nm light, relying on the inherent reactivity of ribonucleotides.

2022-06-09 | PXD031381 | Pride

Conformational coupling of redox-driven Na+ translocation in Vibrio cholerae NADH:quinone oxidoreductase

Project description:Chemical cross-linking coupled to mass spectrometry was used to study the architecture of the NQR complex in absence and presence of the inhibitor DQA (2-decyl-4-quinazolinylamine). The complex was cross-linked with the homobifunctional, noncleavable reagent, disuccinimidyl suberate (DSS).

2023-08-31 | PXD039289 | Pride

LC-MS/MS analysis of an intact synthetic microRNA

Project description:The field of epitranscriptomics is growing in importance, with chemical modification of RNA being associated with a wide variety of biological phenomena. Mass spectrometry (MS) enables the identification of modified RNA residues within their sequence contexts, by using analogous approaches to shotgun proteomics. We have developed a free and open-source database search engine for RNA MS data, called NucleicAcidSearchEngine (NASE), as part of the OpenMS software framework. NASE allows the reliable identification of (modified) RNA sequences from LC-MS/MS data in a high-throughput fashion. For this validation dataset, oligonucleotides with the sequence of mature Drosophila let-7 microRNA, 21 nt in length, were produced synthetically in unmodified and modified (2’-O-methylated at the 3’ uridine) forms. We characterised a 1:1 mixture of both forms of this RNA.

2019-01-10 | PXD012094 | 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