Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of interaction of p97, p37, PPI, SDS22 and Inhibitor-3 using cross-linking mass spectrometry (CL-MS)

ABSTRACT: In this project we investigated the complexes PPI/SDS22/Inhibitor-3 and p97/p37/PPI/SDS22/Inhibitor-3 by CL-MS using DSBU as crosslinker.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Farnusch Kaschani

LAB HEAD: Johannes van den Boom

PROVIDER: PXD026696 | Pride | 2024-11-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20180927_Q2_U1_1-10_WH_SA_DOP_20180924_SPIc-B04.mgf	Mgf
	20180927_Q2_U1_1-10_WH_SA_DOP_20180924_SPIc-B06.mgf	Mgf
	20180927_Q2_U1_1-10_WH_SA_DOP_20180924_SPIc-B08.mgf	Mgf
	20180927_Q2_U1_1-10_WH_SA_DOP_20180924_SPIc-B10.mgf	Mgf
	20180927_Q2_U1_1-2_WH_SA_DOP_20180924_SPIc-B05.mgf	Mgf

Items per page:

1 - 5 of 19

Similar Datasets

dentification of Cross-linking partners of BpA modified p37 and p97 by photo cross-linking MS

Project description:we wanted to see where and how the protein p37 interacts with its partner proteins p97, PPI,Sds22 and I3. To this end p37 derivatives with genetically encoded crosslinking amino acid (p-benzoyl-L-phenylalanine) were generated. After incubation with the partner proteins, photocross-linking and tryptic digest the resulting cross-linked peptides were analysed by mass spectrometry.

2020-10-19 | PXD021182 | Pride

Identification of Cross-linking partners of BpA modified p97 by photo cross-linking MS

Project description:We wanted to see where and how the protein p97 interacts with its partner proteins p37, PPI,Sds22 and I3. To this end a p97 derivative with genetically encoded crosslinking amino acid (p-benzoyl-L-phenylalanine) was generated. After incubation with the partner proteins, photocross-linking and tryptic digest the resulting cross-linked peptides were analysed by mass spectrometry.

2023-07-10 | PXD039939 | Pride

Structural Insights into the Interaction Between Adenovirus 5C Hexon and Human Lactoferrin

Project description:Adenovirus (AdV) infection of the respiratory epithelium is common but poorly understood. Human infective species C AdVs, such as HAdV-C5, utilise the Coxsackie-Adenovirus receptor (CAR) for attachment and subsequently integrins for entry. CAR and integrins are however located deep within the tight junctions in the mucosa where they would not be easily accessible. Recently, a model for CAR-independent AdV entry was proposed. In this model, Lactoferrin (LF), an innate immune protein, aids the viral uptake into epithelial cells by mediating interactions between the major capsid protein, hexon, and yet unknown host cellular receptor(s). Yet, a detailed understanding of the molecular interactions driving this mechanism is lacking. Here, we present a novel cryo-EM structure of HAd-5C hexon at high resolution alongside a hybrid structure of human lactoferrin (hLF) complexed with HAdV-5C hexon. These structures reveal the molecular determinants of the interaction between hLF and HAdV-C5 hexon. hLF engages hexon primarily via its N-terminal Lactoferricin (Lfcin) region, interacting with hexon's hypervariable region 1 (HVR-1). Mutational analyses pinpoint critical Lfcin contacts but also identify additional regions within hLF that critically contribute to hexon binding. Our study sheds more light on the intricate mechanism by which HAdV-C5 utilises soluble hLF/Lfcin for cellular entry. These findings hold promise for advancing gene therapy applications and inform vaccine development.

2024-02-03 | PXD045900 | Pride

Structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in Nucleotide Excision Repair

Project description:TFIIH is a 10-protein complex that is conserved throughout eukaryotes. TFIIH has two primary cellular functions: transcription initiation and nucleotide excision repair (NER). NER in eukaryotes begins by recognition of a bulky lesion by the obligate dimer Rad4-Rad23. This is followed closely by the recruitment of TFIIH which is a structural scaffold, opens a bubble around damaged DNA and scans the damaged strand for bulky lesions. This facilitates the recruitment of two exonucleases which excise the damages strand before an undamaged complement is synthesize. In yeast (Saccharomyces cerevisiae), TFIIH is composed of the two helicases Ssl2 and Rad3, the scaffolding subunits Tfb1, Tfb2, Tfb4 and Ssl1 and the kinase subunits Kin28, Ccl1 and Tfb3, though these later 3 are dispensable for NER.

2021-07-07 | PXD021212 | Pride

Cotranslational activity of the GroEL chaperonin

Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.

2025-10-14 | PXD054379 | Pride

Chemical crosslinking of the SPATA5-SPATA5L1-C1orf109-CINP complex

Project description:Here we present data using chemical crosslinking to inform on the architecture of the SPATA5-SPATA5L1-C1orf109-CINP complex (or the 55LCC).

2024-04-17 | PXD035980 | Pride

An Intrinsically Disordered Region of Ubp10 Governs its Specificity for Deubiquitinating H2A/H2B Dimers over Nucleosomes

Project description:Histone modifications perform a vast array of functions in regulating gene expression, DNA replication, and repair. Monoubiquitination of histone H2B at K123 in yeast (K120 in humans) is an intriguing modification because it is deposited cotranscriptionally, mediates the installation of several other epigenetic marks, and then disappears; hence, it is associated transiently with actively transcribed chromatin. In yeast, the H2B ubiquitin writer is the E2/E3 pair Rad6/Bre1, and there are two deubiquitinases that can erase it, Ubp8 and Ubp10. Whilst Ubp8 resides within the larger SAGA complex, Ubp10 (USP36 in humans) is a monomeric and constitutively active deubiquitinase, raising questions as to what processes regulate it, given it would be undesirable for H2B to be deubiquitinated prematurely before downstream processes connected to this epigenetic mark occur. Here we show that Ubp10’s activity is regulated by acidic regions within its long N-terminal intrinsically disordered region (IDR), which extensively interact with H2A/H2B dimers, as shown by crosslinking mass spectrometry. These interactions vanish when H2A/H2B is present in nucleosomes. These observations explain why Ubp10 has low baseline activity on nucleosomes, but is activated by FACT, a histone chaperone which evicts H2A/H2B dimers from nucleosomes, thereby generating Ubp10’s preferred substrate, which we demonstrate with single molecule fluorescence experiments. Hence, this work provides a biophysical mechanism for how Ubp10 can provide a housekeeping function to deubiquitinate actively-transcribed DNA, wherein FACT produces a temporary pool of H2A/H2B dimers.

2025-07-16 | PXD051971 | Pride

Mechanism of pharmacochaperoning in ATP-sensitive potassium channels revealed by cryo-EM

Project description:ATP-sensitive potassium (K-ATP) channels composed of a pore-forming Kir6.2 potassium channel and a regulatory ABC transporter sulfonylurea receptor 1 (SUR1) regulate insulin secretion in pancreatic beta-cells to maintain glucose homeostasis. Mutations that impair channel folding or assembly prevent cell surface expression and cause congenital hyperinsulinism. Structurally diverse K-ATP inhibitors have been shown to act as pharmacochaperones to correct mutant channel expression, but the mechanism is unknown. Here, we compare cryoEM structures of K-ATP channels bound to pharmacochaperones glibenclamide, repaglinide, and carbamazepine. CyanurBiotinDimercaptoPropionylSuccinimide (CBDPS) cross-linking mass spectrometry was used to partially confirm cryoEM structures.

2019-08-12 | PXD014498 | Pride

An integrative structural biology approach to identify the binding mode of a nanobody towards the pea Ascorbate Peroxidase

Project description:The optimization of diagnostic devices such as biosensors often requires understanding the molecular details of the interaction between capture and target biomolecules. This can be experimentally obtained by cryo-electron microscopy, the preferred method for the analysis of large protein complexes, while NMR and x-ray crystallography are effective for determining the structure of complexes formed by relatively small molecules. Nevertheless, all these approaches are demanding in terms of time and resources and, therefore, we explored the possibility to reduce the experimental load by compensating with in silico modelling. Here we demonstrate that an accurate prediction of the binding mode between a nanobody and its target pea ascorbate peroxidase, an oxidative stress biomarker in plants, can be obtained by combining cross-linking mass spectrometry, hydrogen-deuterium exchange coupled to mass spectrometry and in silico modelling. Such model allowed to precisely design negative mutants that confirmed its accuracy. In conclusion, this study shows that an unconstrained prediction based on deep learning models is still not sufficiently reliable for new targets and difficult-to-model biomolecule classes such as nanobodies, while an experimental-guided approach can provide valuable structural information for lead optimization campaigns of such reagents.

2026-03-10 | PXD070481 | Pride