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Yorodumi- PDB-7yl2: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yl2 | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y07004 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | ANTITUMOR PROTEIN / BRD4(1) / Bromodomain / Inhibitor | ||||||
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: 1.62 Å | ||||||
Authors | Huang, Y. / Wei, A. / Dong, R. / Xu, H. / Zhang, C. / Chen, Z. / Li, J. / Wu, X. / Zhang, Y. / Xu, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y07004 Authors: Huang, Y. / Wei, A. / Dong, R. / Xu, H. / Zhang, C. / Chen, Z. / Li, J. / Wu, X. / Zhang, Y. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yl2.cif.gz | 44.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yl2.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yl2_validation.pdf.gz | 770.6 KB | Display | wwPDB validaton report |
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Full document | 7yl2_full_validation.pdf.gz | 771.8 KB | Display | |
Data in XML | 7yl2_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 7yl2_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/7yl2 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/7yl2 | HTTPS FTP |
-Related structure data
Related structure data | 3mxfS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16767.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-JCO / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-NO3 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.2M Na2NO3, 0.1M HEPES, 20% PEG3350, 10% EtGhly, PH 7.8 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→52.88 Å / Num. obs: 14909 / % possible obs: 91 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.021 / Rrim(I) all: 0.068 / Net I/σ(I): 20.5 / Num. measured all: 149592 / Scaling rejects: 127 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXF Resolution: 1.62→36.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.625 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.71 Å2 / Biso mean: 22.261 Å2 / Biso min: 12.74 Å2
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Refinement step | Cycle: final / Resolution: 1.62→36.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.659 Å / Rfactor Rfree error: 0
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