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Yorodumi- PDB-6se4: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6se4 | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with (+)-JD1, an Organometallic BET Bromodomain Inhibitor | ||||||
Components | Bromodomain-containing protein 4BRD4 | ||||||
Keywords | PROTEIN BINDING / BROMODOMAIN-CONTAINING PROTEIN 4 ISOFORM LONG / BRD4 / BROMODOMAIN / Organometallic BET Bromodomain Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.38 Å | ||||||
Authors | Krojer, T. / Hassell-Hart, S. / Picaud, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Filippakopoulos, P. / Spencer, J. / von Delft, F. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the first bromodomain of human BRD4 in complex with (+)-JD1, an Organometallic BET Bromodomain Inhibitor Authors: Krojer, T. / Hassell-Hart, S. / Picaud, S. / Filippakopoulos, P. / Spencer, J. / von Delft, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6se4.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6se4.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 6se4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/6se4 ftp://data.pdbj.org/pub/pdb/validation_reports/se/6se4 | HTTPS FTP |
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-Related structure data
Related structure data | 3mxfS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.3063129 / Data set type: diffraction image data / Metadata reference: 10.5281/zenodo.3063129 |
-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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-L8W / (+)- | #4: Chemical | #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: 2.16 Å3/Da / Density % sol: 43.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 60% MPD, 0.1M MIB pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→39.51 Å / Num. obs: 27586 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.257 / Mean I/σ(I) obs: 1 / Num. unique obs: 1998 / CC1/2: 0.602 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3MXF Resolution: 1.38→39.51 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.38→39.51 Å
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