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- PDB-7rjo: 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: 7rjo | ||||||||||||
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Title | Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with hnRNPK | ||||||||||||
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![]() | SIGNALING PROTEIN / Brd4 / hnRNPK / acetyllysine | ||||||||||||
Function / homology | ![]() regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / positive regulation of low-density lipoprotein receptor activity / negative regulation of mRNA splicing, via spliceosome / RNA polymerase II C-terminal domain binding / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of DNA damage checkpoint ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / positive regulation of low-density lipoprotein receptor activity / negative regulation of mRNA splicing, via spliceosome / RNA polymerase II C-terminal domain binding / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / RNA processing / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / catalytic step 2 spliceosome / RNA polymerase II CTD heptapeptide repeat kinase activity / mRNA Splicing - Major Pathway / HCMV Late Events / condensed nuclear chromosome / cell projection / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / mRNA splicing, via spliceosome / cytoplasmic stress granule / positive regulation of receptor-mediated endocytosis / 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 / ribonucleoprotein complex / cadherin binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Fedorov, E. / Islam, K. / Ghosh, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization Authors: Wagner, S. / Fedorov, E. / Sudhamalla, B. / Jnawali, H.N. / Debiec, R. / Ghosh, A. / Islam, K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.8 KB | Display | ![]() |
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PDB format | ![]() | 78.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.9 KB | Display | ![]() |
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Full document | ![]() | 463.9 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rjkC ![]() 7rjlC ![]() 7rjmC ![]() 7rjnC ![]() 3mxfS S: Starting model for refinement 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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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#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.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1098.317 Da / Num. of mol.: 1 / Fragment: UNP residues 57-66 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 158 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / | ||||
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#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.78 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.38→24.23 Å / Num. obs: 27852 / % possible obs: 98.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Net I/σ(I): 22.3 / Num. measured all: 263623 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3MXF Resolution: 1.38→24.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.92 / 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: 67.69 Å2 / Biso mean: 25.7296 Å2 / Biso min: 11.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.38→24.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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