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Yorodumi- PDB-5f63: Crystal structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f63 | ||||||
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Title | Crystal structure of the first bromodomain of human BRD4 in complex with SG3-179 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION INHIBITOR / BROMODOMAIN / CAP / HUNK1 / MCAP / PROTEIN BINDING-INHIBITOR COMPLEX / MITOTIC CHROMOSOME ASSOCIATED PROTEIN / CELL CYCLE / INHIBITOR / TRANSCRIPTION-INHIBITOR COMPLEX / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex | ||||||
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 / chromatin / 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: 1.45 Å | ||||||
Authors | Ember, S.W. / Zhu, J.-Y. / Schonbrunn, E. | ||||||
Citation | Journal: Mol. Cancer Ther. / Year: 2017 Title: Potent Dual BET Bromodomain-Kinase Inhibitors as Value-Added Multitargeted Chemical Probes and Cancer Therapeutics. Authors: Ember, S.W. / Lambert, Q.T. / Berndt, N. / Gunawan, S. / Ayaz, M. / Tauro, M. / Zhu, J.Y. / Cranfill, P.J. / Greninger, P. / Lynch, C.C. / Benes, C.H. / Lawrence, H.R. / Reuther, G.W. / ...Authors: Ember, S.W. / Lambert, Q.T. / Berndt, N. / Gunawan, S. / Ayaz, M. / Tauro, M. / Zhu, J.Y. / Cranfill, P.J. / Greninger, P. / Lynch, C.C. / Benes, C.H. / Lawrence, H.R. / Reuther, G.W. / Lawrence, N.J. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f63.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f63.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f63_validation.pdf.gz | 740.7 KB | Display | wwPDB validaton report |
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Full document | 5f63_full_validation.pdf.gz | 742.4 KB | Display | |
Data in XML | 5f63_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 5f63_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f63 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f63 | HTTPS FTP |
-Related structure data
Related structure data | 5f5zC 5f60C 5f61C 5f62C 4o78S C: citing same article (ref.) S: Starting model for refinement |
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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: 15099.380 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O60885 | ||
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#2: Chemical | ChemComp-5W2 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SG3-179 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2015 |
Radiation | Monochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→39.375 Å / Num. obs: 23940 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.11 % / Rmerge F obs: 1 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.038 / Rsym value: 0.035 / Χ2: 0.969 / Net I/σ(I): 37.1 / Num. measured all: 170299 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 5.4 % / Rmerge F obs: 1 / Rmerge(I) obs: 0.017 / Mean I/σ(I) obs: 7.25 / Num. measured obs: 1967 / Num. possible: 321 / Num. unique obs: 319 / Rrim(I) all: 0.018 / Rsym value: 0.218 / Rejects: 0 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4O78 Resolution: 1.45→39.375 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.53 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.39 Å2 / Biso mean: 14.9516 Å2 / Biso min: 3.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→39.375 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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