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Yorodumi- PDB-4pzr: Crystal structure of p300 histone acetyltransferase domain in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pzr | ||||||
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Title | Crystal structure of p300 histone acetyltransferase domain in complex with Coenzyme A | ||||||
Components | Histone acetyltransferase p300 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 / macrophage derived foam cell differentiation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / STAT family protein binding / histone H4 acetyltransferase activity / cellular response to L-leucine / 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 / histone H3K18 acetyltransferase activity / Polo-like kinase mediated events / 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 of T-helper 17 cell lineage commitment / regulation of mitochondrion organization / positive regulation by host of viral transcription / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / regulation of tubulin deacetylation / nuclear androgen receptor binding / acyltransferase activity / internal protein amino acid acetylation / protein acetylation / 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 / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / NF-kappaB binding / histone acetyltransferase complex / Attenuation phase / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / somitogenesis / canonical NF-kappaB signal transduction / pre-mRNA intronic binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / regulation of cellular response to heat / histone acetyltransferase activity / skeletal muscle tissue development / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Regulation of TP53 Activity through Acetylation / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / positive regulation of TORC1 signaling / transcription coregulator binding / CD209 (DC-SIGN) signaling / transcription initiation-coupled chromatin remodeling / negative regulation of autophagy / B cell differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / SUMOylation of transcription cofactors / lung development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||
Authors | Maksimoska, J. / Marmorstein, R. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure of the p300 Histone Acetyltransferase Bound to Acetyl-Coenzyme A and Its Analogues. Authors: Maksimoska, J. / Segura-Pena, D. / Cole, P.A. / Marmorstein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pzr.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pzr.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pzr_validation.pdf.gz | 962.3 KB | Display | wwPDB validaton report |
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Full document | 4pzr_full_validation.pdf.gz | 968.3 KB | Display | |
Data in XML | 4pzr_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4pzr_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/4pzr ftp://data.pdbj.org/pub/pdb/validation_reports/pz/4pzr | HTTPS FTP |
-Related structure data
Related structure data | 4pzsC 4pztC 3biyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43701.688 Da / Num. of mol.: 1 / Fragment: acetyltransferase domain (UNP residues 1287-1664) / Mutation: Y1467F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09472, histone acetyltransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-COA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 16% PEG3350, 3-10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 8, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. all: 24335 / Num. obs: 24262 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rsym value: 0.068 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.099→2.18 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2397 / Rsym value: 0.359 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BIY Resolution: 2.099→31.798 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 23.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→31.798 Å
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Refine LS restraints |
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LS refinement shell |
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