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Yorodumi- PDB-6oie: The double PHD finger (DPF) of MORF in complex with histone H3K14cr -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oie | ||||||
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Title | The double PHD finger (DPF) of MORF in complex with histone H3K14cr | ||||||
Components |
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Keywords | TRANSFERASE / DPF / acetylation / crotonylation | ||||||
Function / homology | Function and homology information histone H3K14 acetyltransferase activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / peptide-lysine-N-acetyltransferase activity / Packaging Of Telomere Ends / histone acetyltransferase activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / histone acetyltransferase ...histone H3K14 acetyltransferase activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / peptide-lysine-N-acetyltransferase activity / Packaging Of Telomere Ends / histone acetyltransferase activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / histone acetyltransferase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / Condensation of Prophase Chromosomes / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / nucleosome assembly / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / chromosome, telomeric region / transcription coactivator activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.075 Å | ||||||
Authors | Klein, B.J. / Kutateladze, T.G. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Authors: Klein, B.J. / Jang, S.M. / Lachance, C. / Mi, W. / Lyu, J. / Sakuraba, S. / Krajewski, K. / Wang, W.W. / Sidoli, S. / Liu, J. / Zhang, Y. / Wang, X. / Warfield, B.M. / Kueh, A.J. / Voss, A.K. ...Authors: Klein, B.J. / Jang, S.M. / Lachance, C. / Mi, W. / Lyu, J. / Sakuraba, S. / Krajewski, K. / Wang, W.W. / Sidoli, S. / Liu, J. / Zhang, Y. / Wang, X. / Warfield, B.M. / Kueh, A.J. / Voss, A.K. / Thomas, T. / Garcia, B.A. / Liu, W.R. / Strahl, B.D. / Kono, H. / Li, W. / Shi, X. / Cote, J. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oie.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oie.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 6oie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oie ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oie | HTTPS FTP |
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-Related structure data
Related structure data | 5u2jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13015.296 Da / Num. of mol.: 2 / Fragment: residues 211-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6B, KIAA0383, MORF, MOZ2, MYST4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYB5, histone acetyltransferase #2: Protein/peptide | Mass: 2144.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16695 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.1-1.3 M sodium citrate tribasic and 0.1 M sodium hepes PH range: 8.4-8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.075→37 Å / Num. obs: 18819 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.08→2.12 Å / Rmerge(I) obs: 0.264 / Num. unique obs: 1810 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U2J Resolution: 2.075→24.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.075→24.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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