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Dataset results
17 results for “substrate binding”
AlphaFold-Multimer (v3) model of a complex of Protein Phosphatase 2A catalytic subunit (PP2A/C), PP2A scaffold subunit (PP2A/A), the B55alpha substrate binding subunit, and FAM122A, a PP2A inhibitor protein.
<p>AlphaFold-Multimer (v3) model structure of a complex of Protein Phosphatase 2A catalytic subunit (PP2A/C), PP2A scaffold subunit (PP2A/A), the B55alpha substrate binding subunit, and FAM122A, a PP2A inhibitor protein. The protein sequences were obtained from UniProt:</p> <p>P67775 · PP2AA_HUMAN</p> <p>P30153 · 2AAA_HUMAN</p> <p>P63151 · 2ABA_HUMAN</p> <p>Q96E09 · PBIR1_HUMAN</p> <p>Coordinates are in mmCIF format. A PyMOL session file is included.</p> <p>Modeling was performed with AlphaFold-Multimer v3, downloaded from DeepMind's github. Structure prediction was performed without templates. The model was relaxed with Amber.</p> <p>FAM122A binds using a short linear motif (SLIM) (residues 84-89) first identified in RBL1 (p107) (Fowle et al., eLife, <a href="https://doi.org/10.7554/eLife.63181">https://doi.org/10.7554/eLife.63181</a> in the form of a short alpha helix (residues 84-92). This is followed by a long alpha helix (residues 96-122) which blocks access to the active site of the catalytic subunit. There are further contacts of FAM122A (residues 150-170) with one of the beta sheets of the B55alpha beta propeller domain. FAM122A regulates PP2A activity during the cell cycle.</p> <p> </p>
Exploring the ligand binding and conformational dynamics of the substrate binding domain 1 of the ABC transporter GlnPQ
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Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
<p>Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.</p>
Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3. Blaimschein et al.: Data sets
<p>Data sets used in the manuscript 'Substrate-Binding Guides Individual Melibiose Permeases MelB to Structurally Soften and to Destabilize Cytoplasmic Middle-Loop C3' by Blaimschein et al.</p> <p>The analysis scripts can be found at https://doi.org/10.5281/zenodo.7268838</p>
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK RNA-Seq)
GEO Series GSE55326. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL RNA-Seq)
GEO Series GSE55329. Caenorhabditis elegans. 3 samples. Type: Expression profiling by high throughput sequencing.
CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 1]
GEO Series GSE112781. Mus musculus. 7 samples. Type: Other.
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL PAR-CLIP)
GEO Series GSE55325. Caenorhabditis elegans. 3 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing.
CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 2]
GEO Series GSE112822. Mus musculus. 36 samples. Type: Other.
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK PAR-CLIP)
GEO Series GSE55324. Homo sapiens. 3 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing.
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL small RNA)
GEO Series GSE55332. Caenorhabditis elegans. 2 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing.
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates
GEO Series GSE55333. Caenorhabditis elegans; Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing.
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (small RNA AGO-IP)
GEO Series GSE55331. Homo sapiens. 2 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing.
CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning
GEO Series GSE113023. Mus musculus. 78 samples. Type: Other.
CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning [dataset 3]
GEO Series GSE113022. Mus musculus. 35 samples. Type: Other.
VOLATILE4ARCHAEO:Sublimation rate or volatile binding media on substrates
<p>Sublimation dataset of selected of volatile binding media</p>
ARRIVE guidelines author checklist of "Structural and functional analysis reveals the catalytic mechanism and substrate binding mode of the broad-spectrum endolysin Ply2741"
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.