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Yorodumi- PDB-8qap: Crystal Structure of the first bromodomain of BRD4 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qap | ||||||
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Title | Crystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 2 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 8qap.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qap.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qap_validation.pdf.gz | 713.1 KB | Display | wwPDB validaton report |
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Full document | 8qap_full_validation.pdf.gz | 713.4 KB | Display | |
Data in XML | 8qap_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 8qap_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/8qap ftp://data.pdbj.org/pub/pdb/validation_reports/qa/8qap | HTTPS FTP |
-Related structure data
Related structure data | 8qalC 8qanC 8qarC 8qazC 8qb0C 8qb2C 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
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 / Mutation: First bromodomain (residues 1796-1899) Source method: isolated from a genetically manipulated source Details: The first two residues SM derive from the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O60885 | ||||
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#2: Chemical | ChemComp-Q9U / Mass: 317.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N5OS / Feature type: SUBJECT OF INVESTIGATION | ||||
#3: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 16% PEG 3350, 20% ethylene glycol |
-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 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.37 Å / Num. obs: 26131 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Rrim(I) all: 0.114 / Χ2: 0.95 / Net I/σ(I): 12.5 / Num. measured all: 318947 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 1.449 / Num. measured all: 16195 / Num. unique obs: 1286 / CC1/2: 0.767 / Rpim(I) all: 0.422 / Rrim(I) all: 1.511 / Χ2: 0.88 / Net I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→39.002 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.76 / 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: 1.4→39.002 Å
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Refine LS restraints |
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LS refinement shell |
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