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- PDB-6gyt: Transcription factor dimerization activates the p300 acetyltransferase -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gyt | |||||||||
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Title | Transcription factor dimerization activates the p300 acetyltransferase | |||||||||
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![]() | GENE REGULATION / P300 / CBP / acetyltransferase / Chromatin / transcriptional regulation | |||||||||
Function / homology | ![]() 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 / histone H2B acetyltransferase activity ...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 / histone H2B acetyltransferase activity / thigmotaxis / 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 / cellular response to L-leucine / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / acetylation-dependent protein binding / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / regulation of androgen receptor signaling pathway / positive regulation by host of viral transcription / regulation of mitochondrion organization / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / face morphogenesis / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / megakaryocyte development / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / macrophage derived foam cell differentiation / nuclear androgen receptor binding / regulation of tubulin deacetylation / STAT family protein binding / internal protein amino acid acetylation / acyltransferase activity / protein acetylation / positive regulation of transforming growth factor beta receptor signaling pathway / fat cell differentiation / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / RUNX3 regulates p14-ARF / acetyltransferase activity / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Attenuation phase / canonical NF-kappaB signal transduction / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / somitogenesis / positive regulation of T-helper 17 cell lineage commitment / pre-mRNA intronic binding / regulation of cellular response to heat / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / histone acetyltransferase activity / skeletal muscle tissue development / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Regulation of TP53 Activity through Acetylation / positive regulation of TORC1 signaling / RORA activates gene expression / CD209 (DC-SIGN) signaling / negative regulation of autophagy / B cell differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / SUMOylation of transcription cofactors / regulation of signal transduction by p53 class mediator / regulation of autophagy Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Panne, D. / Ortega, E. | |||||||||
![]() | ![]() Title: Transcription factor dimerization activates the p300 acetyltransferase. Authors: Ortega, E. / Rengachari, S. / Ibrahim, Z. / Hoghoughi, N. / Gaucher, J. / Holehouse, A.S. / Khochbin, S. / Panne, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.2 KB | Display | ![]() |
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PDB format | ![]() | 111.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460 KB | Display | ![]() |
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Full document | ![]() | 468.6 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gyrC ![]() 4bhwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18970.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q09472, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
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#2: Protein | Mass: 19586.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q09472, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
#3: Protein/peptide | Mass: 841.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Diacetylated histone H4 peptide / Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.83 % |
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Crystal grow | Temperature: 294 K / Method: evaporation / Details: 1.6 M Ammonium Sulfate, 100 mM Bicine, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.6 Å / Num. obs: 23996 / % possible obs: 97.29 % / Redundancy: 9.1 % / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.5→2.6 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BHW Resolution: 2.5→46.087 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 40.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.087 Å
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Refine LS restraints |
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LS refinement shell |
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