[English] 日本語
Yorodumi- PDB-5f61: Crystal structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f61 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the first bromodomain of human BRD4 in complex with MA4-022-1 | ||||||
Components | Bromodomain-containing protein 4BRD4 | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION INHIBITOR / ROMODOMAIN / CAP / HUNK1 / MCAP / PROTEIN BINDING-INHIBITOR COMPLEX / MITOTIC CHROMOSOME ASSOCIATED PROTEIN / CELL CYCLE / INHIBITOR / 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 / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5f61.cif.gz | 177.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5f61.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 5f61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f61 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f61 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5f5zC 5f60C 5f62C 5f63C 4o78S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 2 / 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 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.31 % |
---|---|
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 MA4-022-1 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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→39.255 Å / Num. obs: 43128 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 7.36 % / Biso Wilson estimate: 10.48 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.063 / Rsym value: 0.059 / Χ2: 0.97 / Net I/σ(I): 25 / Num. measured all: 317302 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 2.95 % / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 5 / Num. measured obs: 3759 / Num. possible: 524 / Num. unique obs: 516 / Rrim(I) all: 0.039 / Rsym value: 0.2 / Rejects: 0 / % possible all: 93.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O78 Resolution: 1.45→39.255 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.86 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→39.255 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|