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Yorodumi- PDB-5igk: Crystal structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5igk | ||||||
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Title | Crystal structure of the first bromodomain of human BRD4 in complex with bromosporine (BSP) | ||||||
Components | Bromodomain-containing protein 4BRD4 | ||||||
Keywords | TRANSCRIPTION / post translational modifications / BET family / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / transcription coregulator activity ...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 / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Felletar, I. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci Adv / Year: 2016 Title: Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Authors: Picaud, S. / Leonards, K. / Lambert, J.P. / Dovey, O. / Wells, C. / Fedorov, O. / Monteiro, O. / Fujisawa, T. / Wang, C.Y. / Lingard, H. / Tallant, C. / Nikbin, N. / Guetzoyan, L. / Ingham, ...Authors: Picaud, S. / Leonards, K. / Lambert, J.P. / Dovey, O. / Wells, C. / Fedorov, O. / Monteiro, O. / Fujisawa, T. / Wang, C.Y. / Lingard, H. / Tallant, C. / Nikbin, N. / Guetzoyan, L. / Ingham, R. / Ley, S.V. / Brennan, P. / Muller, S. / Samsonova, A. / Gingras, A.C. / Schwaller, J. / Vassiliou, G. / Knapp, S. / Filippakopoulos, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5igk.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5igk.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 5igk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/5igk ftp://data.pdbj.org/pub/pdb/validation_reports/ig/5igk | HTTPS FTP |
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-Related structure data
Related structure data | 5iglC 5igmC 2grcS 2oo1S 2ossS 2ouoS 3d7cS 3daiS S: Starting model for refinement C: citing same article (ref.) |
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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 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) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-BMF / |
#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: 2.24 Å3/Da / Density % sol: 45.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Na/K(tart), 0.1 M BTProp pH 8.5, 20% PEG3350, 10% EtGly PH range: 7.5 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.5 Å / Num. obs: 15007 / % possible obs: 97.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.022 / Net I/av σ(I): 21.1 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5.9 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C Resolution: 1.7→19.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.155 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.287 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→19.5 Å
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Refine LS restraints |
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