+Open data
-Basic information
Entry | Database: PDB / ID: 5trm | ||||||
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Title | Crystal structure of human GCN5 histone acetyltransferase domain | ||||||
Components | Histone acetyltransferase KAT2A | ||||||
Keywords | TRANSFERASE / apo | ||||||
Function / homology | Function and homology information 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 / regulation of DNA repair / negative regulation of gluconeogenesis / 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 protein stability / regulation of synaptic plasticity / 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 / Ub-specific processing proteases / regulation of cell cycle / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Guo, Y.R. / Tao, Y.J. | ||||||
Citation | Journal: Nature / Year: 2017 Title: KAT2A coupled with the alpha-KGDH complex acts as a histone H3 succinyltransferase. Authors: Wang, Y. / Guo, Y.R. / Liu, K. / Yin, Z. / Liu, R. / Xia, Y. / Tan, L. / Yang, P. / Lee, J.H. / Li, X.J. / Hawke, D. / Zheng, Y. / Qian, X. / Lyu, J. / He, J. / Xing, D. / Tao, Y.J. / Lu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5trm.cif.gz | 755.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5trm.ent.gz | 635.7 KB | Display | PDB format |
PDBx/mmJSON format | 5trm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5trm_validation.pdf.gz | 622.6 KB | Display | wwPDB validaton report |
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Full document | 5trm_full_validation.pdf.gz | 696.7 KB | Display | |
Data in XML | 5trm_validation.xml.gz | 131.9 KB | Display | |
Data in CIF | 5trm_validation.cif.gz | 176.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/5trm ftp://data.pdbj.org/pub/pdb/validation_reports/tr/5trm | HTTPS FTP |
-Related structure data
Related structure data | 5trlC 1z4rS 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: 19406.660 Da / Num. of mol.: 24 / Fragment: catalytic domain, UNP residues 497-662 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2A, GCN5, GCN5L2, HGCN5 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92830, histone acetyltransferase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 1.8M Sodium formate, 0.1M Sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 117491 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 43.66 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Χ2: 1.048 / Net I/av σ(I): 15.05 / Net I/σ(I): 6.3 / Num. measured all: 726744 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1z4r Resolution: 2.9→48.179 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.45 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.23 Å2 / Biso mean: 32.5282 Å2 / Biso min: 3.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→48.179 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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