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Yorodumi- PDB-7fh2: Crystal structure of the first bromodomain of BRD4 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fh2 | ||||||
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Title | Crystal structure of the first bromodomain of BRD4 in complex with 16D10 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / BROMODOMAIN / BRD4 / HISTONE | ||||||
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: 2.492 Å | ||||||
Authors | Yokoyama, T. / Hirasawa, N. | ||||||
Citation | Journal: Biochem Pharmacol / Year: 2021 Title: A chalcone derivative suppresses TSLP induction in mice and human keratinocytes through binding to BET family proteins. Authors: Segawa, R. / Takeda, H. / Yokoyama, T. / Ishida, M. / Miyata, C. / Saito, T. / Ishihara, R. / Nakagita, T. / Sasano, Y. / Kanoh, N. / Iwabuchi, Y. / Mizuguchi, M. / Hiratsuka, M. / Hirasawa, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fh2.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fh2.ent.gz | 161.1 KB | Display | PDB format |
PDBx/mmJSON format | 7fh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fh2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7fh2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7fh2_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 7fh2_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/7fh2 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/7fh2 | HTTPS FTP |
-Related structure data
Related structure data | 6ajwS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 16160.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 #2: Chemical | ChemComp-4JI / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 13.4 mg/mL BRD4-BD1, 0.5 mM 16D10, 20% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→47.53 Å / Num. obs: 21984 / % possible obs: 99.27 % / Redundancy: 10.9 % / CC1/2: 0.998 / Rpim(I) all: 0.038 / Rrim(I) all: 0.125 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.49→2.58 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2089 / CC1/2: 0.953 / Rpim(I) all: 0.371 / Rrim(I) all: 1.254 / % possible all: 95.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AJW Resolution: 2.492→19.63 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.52 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.492→19.63 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: 11.618 Å / Origin y: 0.485 Å / Origin z: 10.533 Å
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Refinement TLS group |
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