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Yorodumi- PDB-5lku: Crystal structure of the p300 acetyltransferase catalytic core wi... -
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-Basic information
Entry | Database: PDB / ID: 5lku | ||||||
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Title | Crystal structure of the p300 acetyltransferase catalytic core with coenzyme A. | ||||||
Components | Histone acetyltransferase p300,Histone acetyltransferase p300 | ||||||
Keywords | TRANSFERASE / p300 acetyltransferase / CoA / chromatin modification / acylation | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Kaczmarska, Z. / Ortega, E. / Marquez, J.A. / Panne, D. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2017 Title: Structure of p300 in complex with acyl-CoA variants. Authors: Kaczmarska, Z. / Ortega, E. / Goudarzi, A. / Huang, H. / Kim, S. / Marquez, J.A. / Zhao, Y. / Khochbin, S. / Panne, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lku.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lku.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 5lku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lku_validation.pdf.gz | 704 KB | Display | wwPDB validaton report |
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Full document | 5lku_full_validation.pdf.gz | 707.3 KB | Display | |
Data in XML | 5lku_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5lku_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/5lku ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lku | HTTPS FTP |
-Related structure data
Related structure data | 5lktC 5lkxC 5lkzC 4bhwS S: Starting model for refinement C: citing same article (ref.) |
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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: 67102.695 Da / Num. of mol.: 1 / Mutation: Y1467F,Y1467F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09472, histone acetyltransferase | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-COA / | #4: 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: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Tris, PEG MME 2000 / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50.01 Å / Num. obs: 10571 / % possible obs: 99.7 % / Redundancy: 7.04 % / Rrim(I) all: 0.383 / Net I/σ(I): 5.65 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 7.34 % / Mean I/σ(I) obs: 2.29 / Rrim(I) all: 1.128 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BHW Resolution: 3.5→50.01 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.867 / SU B: 30.551 / SU ML: 0.467 / Cross valid method: THROUGHOUT / ESU R Free: 0.583 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.299 Å2
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Refinement step | Cycle: 1 / Resolution: 3.5→50.01 Å
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