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Yorodumi- PDB-7d0s: Crystal structure of human HBO1-BRPF2 in complex with succinyl-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d0s | ||||||
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Title | Crystal structure of human HBO1-BRPF2 in complex with succinyl-coenzyme A | ||||||
Components |
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Keywords | TRANSFERASE / histone acetyltransferase / complex / HBO1 / BRPF2 / succinyl-CoA / acylation | ||||||
Function / homology | Function and homology information histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K5 acetyltransferase activity ...histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / natural killer cell differentiation / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / regulation of nucleotide-excision repair / positive regulation of DNA-templated transcription, elongation / histone H3-K14 acetyltransferase complex / regulation of DNA-templated DNA replication initiation / stress-activated protein kinase signaling cascade / DNA replication origin binding / site of DNA damage / regulation of DNA replication / chromosome, centromeric region / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of DNA replication / regulation of cell growth / transcription coregulator activity / positive regulation of protein localization to nucleus / chromosome / HATs acetylate histones / DNA replication / regulation of cell cycle / DNA repair / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Li, W. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: HBO1 is a versatile histone acyltransferase critical for promoter histone acylations. Authors: Xiao, Y. / Li, W. / Yang, H. / Pan, L. / Zhang, L. / Lu, L. / Chen, J. / Wei, W. / Ye, J. / Li, J. / Li, G. / Zhang, Y. / Tan, M. / Ding, J. / Wong, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d0s.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d0s.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 7d0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/7d0s ftp://data.pdbj.org/pub/pdb/validation_reports/d0/7d0s | HTTPS FTP |
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-Related structure data
Related structure data | 7d0oC 7d0pC 7d0qC 7d0rC 5gk9S 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: 32596.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KAT7, HBO1, HBOa, MYST2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95251, histone acetyltransferase |
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#2: Protein/peptide | Mass: 5699.317 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86X06 |
#3: Chemical | ChemComp-SCA / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.2 M L-Proline, 0.1 M HEPES, pH 7.5, 24% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50.01 Å / Num. obs: 16040 / % possible obs: 94.7 % / Redundancy: 5.8 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1280 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GK9 Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.321 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.3 Å2 / Biso mean: 63.503 Å2 / Biso min: 27.69 Å2
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Refinement step | Cycle: final / Resolution: 2.3→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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