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- PDB-6djc: Crystal structure of human Bromodomain-containing protein 4 (BRD4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6djc | ||||||
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Title | Crystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS645 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION/INHIBITOR / transcription / inhibitor / histone acetylation / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, C. / Zhou, M.M. | ||||||
![]() | ![]() Title: Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth. Authors: Ren, C. / Zhang, G. / Han, F. / Fu, S. / Cao, Y. / Zhang, F. / Zhang, Q. / Meslamani, J. / Xu, Y. / Ji, D. / Cao, L. / Zhou, Q. / Cheung, K.L. / Sharma, R. / Babault, N. / Yi, Z. / Zhang, W. ...Authors: Ren, C. / Zhang, G. / Han, F. / Fu, S. / Cao, Y. / Zhang, F. / Zhang, Q. / Meslamani, J. / Xu, Y. / Ji, D. / Cao, L. / Zhou, Q. / Cheung, K.L. / Sharma, R. / Babault, N. / Yi, Z. / Zhang, W. / Walsh, M.J. / Zeng, L. / Zhou, M.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.8 KB | Display | ![]() |
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PDB format | ![]() | 104.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6dneC ![]() 3zyuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15687.110 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: proteolysis during crystallization / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CF6 / | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | The complete crystallized sequence was: ...The complete crystallized sequence was: SMNPPPPETS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH6.5, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08754 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 50373 / % possible obs: 92.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Net I/σ(I): 53.6 |
Reflection shell | Resolution: 1.46→1.49 Å / Rmerge(I) obs: 0.914 / Rpim(I) all: 0.281 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZYU Resolution: 1.46→37.323 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 16.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→37.323 Å
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Refine LS restraints |
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LS refinement shell |
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