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Yorodumi- PDB-8qb2: Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qb2 | ||||||
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Title | Crystal Structure of BRPF1 bromodomain in complex with acetyl-pyrrole derivative compound 79 | ||||||
Components | Peregrin | ||||||
Keywords | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | Function and homology information acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Dalle Vedove, A. / Cazzanelli, G. / Lolli, G. | ||||||
Funding support | Italy, 1items
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Citation | Journal: To be published Title: Dual BET/BRPF1 inhibitors induce morphological alteration and cellular death in various human cancer cell lines Authors: Cazzanelli, G. / Dalle Vedove, A. / Caflisch, A. / Lolli, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qb2.cif.gz | 87 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qb2.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qb2_validation.pdf.gz | 781.1 KB | Display | wwPDB validaton report |
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Full document | 8qb2_full_validation.pdf.gz | 781.9 KB | Display | |
Data in XML | 8qb2_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 8qb2_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/8qb2 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/8qb2 | HTTPS FTP |
-Related structure data
Related structure data | 8qalC 8qanC 8qapC 8qarC 8qazC 8qb0C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13703.698 Da / Num. of mol.: 1 / Mutation: bromodomain (residues 626-740) Source method: isolated from a genetically manipulated source Details: First residue S derives from the expression tag / Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P55201 |
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#2: Chemical | ChemComp-GKI / |
#3: Chemical | ChemComp-NO3 / |
#4: 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: 2.4 Å3/Da / Density % sol: 48.72 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.18 M sodium nitrate, 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→62.23 Å / Num. obs: 25337 / % possible obs: 100 % / Redundancy: 18 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.01 / Rrim(I) all: 0.042 / Χ2: 0.99 / Net I/σ(I): 31 / Num. measured all: 456899 |
Reflection shell | Resolution: 1.42→1.45 Å / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 1.601 / Num. measured all: 24023 / Num. unique obs: 1281 / CC1/2: 0.821 / Rpim(I) all: 0.377 / Rrim(I) all: 1.645 / Χ2: 0.97 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→52.386 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.55 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→52.386 Å
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Refine LS restraints |
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LS refinement shell |
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