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Open data
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Basic information
Entry | Database: PDB / ID: 8e6o | ||||||
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Title | Crystal structure of human GCN5 histone acetyltransferase domain | ||||||
![]() | Histone acetyltransferase KAT2A | ||||||
![]() | TRANSFERASE / histone acetyltransferase | ||||||
Function / homology | ![]() histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation ...histone succinyltransferase activity / peptidyl-lysine glutarylation / histone glutaryltransferase activity / metencephalon development / regulation of cartilage development / positive regulation of cell projection organization / : / histone H4K12 acetyltransferase activity / histone H3K9 acetyltransferase activity / positive regulation of cardiac muscle cell differentiation / regulation of bone development / regulation of stem cell population maintenance / negative regulation of centriole replication / regulation of regulatory T cell differentiation / transcription factor TFTC complex / telencephalon development / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / histone H3K18 acetyltransferase activity / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Cardiogenesis / SAGA complex / limb development / NOTCH4 Intracellular Domain Regulates Transcription / regulation of T cell activation / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / midbrain development / regulation of tubulin deacetylation / intracellular distribution of mitochondria / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / Formation of paraxial mesoderm / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / histone acetyltransferase complex / long-term memory / negative regulation of gluconeogenesis / regulation of DNA repair / somitogenesis / histone acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to nutrient levels / cellular response to nerve growth factor stimulus / positive regulation of cytokine production / neural tube closure / gluconeogenesis / regulation of synaptic plasticity / regulation of protein stability / B-WICH complex positively regulates rRNA expression / multicellular organism growth / response to organic cyclic compound / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to tumor necrosis factor / heart development / HATs acetylate histones / fibroblast proliferation / protein phosphatase binding / DNA-binding transcription factor binding / in utero embryonic development / transcription coactivator activity / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lu, X.T. / Tao, Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human GCN5 histone acetyltransferase domain Authors: Lu, X.T. / Tao, Y.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 91.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5trlS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19205.479 Da / Num. of mol.: 3 / Fragment: catalytic domain, UNP residues 497-662 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q92830, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | Mass: 839.597 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H40N7O18P3S / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1 M Succinic acid pH 7.0, 0.1 M HEPES pH 7, and 1% w/v PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.37→50 Å / Num. obs: 30628 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 44.55 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Χ2: 1.298 / Net I/σ(I): 9.4 / Num. measured all: 385378 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TRL Resolution: 2.37→43.6 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3862 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→43.6 Å
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Refine LS restraints |
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LS refinement shell |
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