Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular view of ER membrane remodeling by the Sec61/TRAP translocon

ABSTRACT: Cross-linking mass spectrometry of the sheep Sec61-TRAP complex

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Ovis Aries (ncbitaxon:9940)

SUBMITTER: Ville Paavilainen

PROVIDER: MSV000090438 | MassIVE |

SECONDARY ACCESSION(S): PXD037125

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Similar Datasets

Prenociceptin TRAP

Project description:Prenociceptin TRAP

| PRJNA428727 | ENA

Molecular Architecture of the Yeast Mediator Complex

Project description:Cross-linking MS data from the yeast Mediator complex. Cross-linking was performed using either BS3 or 1:1 mix of d0:d12 DSS. Includes unfractionated, SEC enriched, high pH reverse phase fractionated, DDA and inclusion list generated files.

2015-08-13 | MSV000079237 | MassIVE

Rapid molecular profiling of defined cell types using viral TRAP

Project description:Translational profiling methodologies enable the systematic characterization of cell types in complex tissues such as the mammalian brain, where neuronal isolation is exceptionally difficult. Here, we report a versatile strategy to profile CNS cell types in a spatiotemporally-restricted fashion by engineering a Cre-dependent adeno-associated virus expressing an EGFP-tagged ribosomal protein (AAV-FLEX-EGFPL10a) to access translating mRNAs by TRAP. We demonstrate the utility of this AAV to target a variety of genetically and anatomically defined neural populations expressing Cre recombinase and illustrate the ability of this viral TRAP (vTRAP) approach to recapitulate the molecular profiles obtained by bacTRAP in corticothalamic neurons across multiple serotypes. Furthermore, spatially restricting AAV injections enabled the elucidation of regional differences in gene expression within this cell type. Taken together, these results establish the broad applicability of the vTRAP strategy for the molecular dissection of any CNS or peripheral cell type that can be engineered to express Cre.

2017-04-10 | GSE89737 | GEO

VEGF Trap in Treating Patients With Previously Treated Metastatic Colorectal Cancer

Project description:This phase II trial is studying how well VEGF Trap works in treating patients with previously treated metastatic colorectal cancer. VEGF Trap may stop the growth of colorectal cancer by blocking blood flow to the tumor.

| 2035047 | ecrin-mdr-crc

Molecular snapshots of translation and protein translocation at the ER membrane

Project description:The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome . It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. While individual components of this machine have been studied at high resolution in isolation, insights into their interplay in the native membrane remain limited. Here, we use electron cryo-tomography (cryo-ET), extensive classification and molecular modeling to capture molecular resolution snapshots of mRNA translation and protein maturation at the ER membrane. Comprehensively recapitulating the translational elongation cycle, we identify a highly abundant classical pre-translocation (PRE) intermediate with eEF1a in an extended conformation following the decoding state, which indicates that eEF1a remains ribosome-associated after GTP-hydrolysis during proofreading. The complete atomic structure of the most abundant ER translocon variant comprising the protein-conducting channel Sec61, the translocon-associated protein complex (TRAP) and the oligosaccharyltransferase complex A (OSTA) reveals the molecular framework for signal peptide (SP) membrane insertion and protein N-glycosylation. Associated with OSTA we observe stoichiometric and sub-stoichiometric cofactors, likely including protein isomerases. Collectively, comprehensive analysis of ER-associated protein biogenesis ex vivo reveals numerous mechanistic insights advancing beyond the study of isolated components.

2023-02-03 | PXD035475 | Pride

Trap-80-dependence of TNF-alpha-induced genes

Project description:In fibroblasts, p65-dependent genes can be sub-divided, depending on whether they are Trap-80-dependent or -independent. To examine the generality of this grouping, we performed a microarray analysis of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation of NF-kappaB activity using TNF-alpha. RNA was extracted from three independent cultures of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation for 1 hour with 5ng/ml TNF-alpha. The unstimulated and stimulated wild-type samples, and the stimulated Trap-80 knock-down samples, were used for microarray analysis.

2010-04-09 | E-GEOD-12697 | biostudies-arrayexpress

Substrates of human TRAP complex

Project description:While the Sec61-complex in the membrane of the human endoplasmic reticulum facilitates translocation of all precursor polypeptides with amino-terminal signal peptides or transmembrane helices, the Sec61-associated translocon-associated protein (TRAP)-complex supports translocation of only a subset of precursor polypeptides, i.e. in a substrate-specific manner. To characterize TRAP-dependent precursors, we combined siRNA-mediated TRAP depletion in HeLa cells, label-free quantitative proteomics, and differential expression analysis. Sec61 served as a positive control

2018-08-09 | PXD008178 | Pride

TRAP-seq following Pdx1 depletion

Project description:TRAP performed in GFP-RPL10A Min6 cells transfected with siRNA targeting Pdx1 or a non-targeting (NT) control. IP RNA was isolated by TRAP protocol and input lysate was used to isolate Total RNA. RNA-seq was performed on both IP and Total RNA.

2019-08-16 | GSE115219 | GEO

CX DHPG TRAP-seq

Project description:CX DHPG TRAP-seq

| PRJNA827184 | ENA

Transcriptional profiling of pyramidal neurons in the cerebral cortex of Glt25d2-TRAP (DU9) mice administered either saline or cocaine [TRAP-seq]

Project description:TRAP translational profiling is a method that allows investigators to genetically characterize specific cell types in complex tissues such as mouse brain. Using this technique we obtained RNA-Seq data from actively translating transcripts present in pyramidal neurons in the cerebral cortex of adult Glt25d2-EGFP/Rpl10a (DU9) mice that were administered either saline or cocaine.

2019-12-16 | GSE141337 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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