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- PDB-7d0q: Crystal structure of human HBO1-BRPF2 in complex with butyryl-coe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d0q | ||||||
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Title | Crystal structure of human HBO1-BRPF2 in complex with butyryl-coenzyme A | ||||||
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![]() | TRANSFERASE / histone acetyltransferase / complex / HBO1 / BRPF2 / butyryl-CoA / acylation | ||||||
Function / homology | ![]() 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 H4K12 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 H4K12 acetyltransferase activity / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / natural killer cell differentiation / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / regulation of nucleotide-excision repair / stress-activated protein kinase signaling cascade / positive regulation of DNA-templated transcription, elongation / histone H3-K14 acetyltransferase complex / regulation of DNA-templated DNA replication initiation / MOZ/MORF histone acetyltransferase complex / regulation of DNA replication / site of DNA damage / DNA replication origin binding / 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 / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, W. / Ding, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.1 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.1 KB | Display | ![]() |
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Full document | ![]() | 763.7 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d0oC ![]() 7d0pC ![]() 7d0rC ![]() 7d0sC ![]() 5gk9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 32596.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 58 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/BCO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BCO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-BCO / |
#5: Chemical | ChemComp-CL / |
#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, 20% w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50.01 Å / Num. obs: 18377 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1836 / CC1/2: 0.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GK9 Resolution: 2.21→50.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 18.039 / SU ML: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 157.83 Å2 / Biso mean: 69.279 Å2 / Biso min: 33.17 Å2
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Refinement step | Cycle: final / Resolution: 2.21→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.211→2.268 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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