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Yorodumi- PDB-8e1d: NMR-derived ensemble of the TAZ2 domain of p300 bound to the micr... -
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-Basic information
Entry | Database: PDB / ID: 8e1d | ||||||
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Title | NMR-derived ensemble of the TAZ2 domain of p300 bound to the microphthalmia-associated transcription factor | ||||||
Components |
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Keywords | TRANSCRIPTION/TRANSFERASE / TAZ2 / MITF / METAL BINDING PROTEIN / TRANSCRIPTION-TRANSFERASE complex | ||||||
Function / homology | Function and homology information melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation ...melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / thigmotaxis / histone H2B acetyltransferase activity / regulation of RNA biosynthetic process / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / melanocyte differentiation / regulation of osteoclast differentiation / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / cellular response to L-leucine / histone H3 acetyltransferase activity / bone remodeling / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NGF-stimulated transcription / NFE2L2 regulating inflammation associated genes / Regulation of MITF-M-dependent genes involved in apoptosis / TGFBR3 expression / STAT3 nuclear events downstream of ALK signaling / histone H3K18 acetyltransferase activity / camera-type eye development / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / Polo-like kinase mediated events / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / positive regulation by host of viral transcription / face morphogenesis / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / regulation of glycolytic process / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / FOXO-mediated transcription of cell death genes / Regulation of NFE2L2 gene expression / megakaryocyte development / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / TRAF6 mediated IRF7 activation / NFE2L2 regulating anti-oxidant/detoxification enzymes / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating tumorigenic genes / macrophage derived foam cell differentiation / regulation of tubulin deacetylation / nuclear androgen receptor binding / STAT family protein binding / acyltransferase activity / protein acetylation / internal protein amino acid acetylation / stimulatory C-type lectin receptor signaling pathway / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation / E-box binding / acetyltransferase activity / Regulation of MITF-M-dependent genes involved in pigmentation / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / SUMOylation of transcription factors / NF-kappaB binding / histone acetyltransferase complex / cell fate commitment / somitogenesis / Attenuation phase / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of gluconeogenesis / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / canonical NF-kappaB signal transduction / positive regulation of T-helper 17 cell lineage commitment Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Langelaan, D.N. / Branch, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Biochim Biophys Acta Mol Cell Res / Year: 2023 Title: Structural basis of CBP/p300 recruitment by the microphthalmia-associated transcription factor. Authors: Brown, A.D. / Vergunst, K.L. / Branch, M. / Blair, C.M. / Dupre, D.J. / Baillie, G.S. / Langelaan, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e1d.cif.gz | 747.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e1d.ent.gz | 625.1 KB | Display | PDB format |
PDBx/mmJSON format | 8e1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e1d_validation.pdf.gz | 569.6 KB | Display | wwPDB validaton report |
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Full document | 8e1d_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8e1d_validation.xml.gz | 128.8 KB | Display | |
Data in CIF | 8e1d_validation.cif.gz | 154.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/8e1d ftp://data.pdbj.org/pub/pdb/validation_reports/e1/8e1d | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3720.123 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MITF, BHLHE32 / Production host: Escherichia coli (E. coli) / References: UniProt: O75030 | ||
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#2: Protein | Mass: 10107.916 Da / Num. of mol.: 1 / Mutation: C1738A C1746A C1789A C1790A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Escherichia coli (E. coli) References: UniProt: Q09472, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
#3: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 20 mM / Label: condition 1 / pH: 6 / Pressure: 1 atm / Temperature: 308 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 4 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |