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Open data
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Basic information
Entry | Database: PDB / ID: 8fvk | ||||||
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Title | First bromodomain of BRD4 liganded with CCS-1477 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION/INHIBITOR / bromodomain / small molecule ligand / complex / TRANSCRIPTION / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schonbrunn, E. / Bikowitz, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition. Authors: Shendy, N.A.M. / Bikowitz, M. / Sigua, L.H. / Zhang, Y. / Mercier, A. / Khashana, Y. / Nance, S. / Liu, Q. / Delahunty, I.M. / Robinson, S. / Goel, V. / Rees, M.G. / Ronan, M.A. / Wang, T. / ...Authors: Shendy, N.A.M. / Bikowitz, M. / Sigua, L.H. / Zhang, Y. / Mercier, A. / Khashana, Y. / Nance, S. / Liu, Q. / Delahunty, I.M. / Robinson, S. / Goel, V. / Rees, M.G. / Ronan, M.A. / Wang, T. / Kocak, M. / Roth, J.A. / Wang, Y. / Freeman, B.B. / Orr, B.A. / Abraham, B.J. / Roussel, M.F. / Schonbrunn, E. / Qi, J. / Durbin, A.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fv2C ![]() 8fvfC ![]() 8fvsC ![]() 8fxaC ![]() 8fxeC ![]() 8fxoC ![]() 8g6tC ![]() 8ga2C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 2 / Fragment: bromodomain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Ammonium sulfate, 0.1M Tris pH8.5, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→34.2 Å / Num. obs: 41819 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.53→34.2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2997 / CC1/2: 0.9 / Rrim(I) all: 0.503 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.53→34.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.496 Å / Origin y: -15.1096 Å / Origin z: -12.8705 Å
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Refinement TLS group | Selection details: all |