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- PDB-7tv0: Crystal structure of BRD4 bromodomain 1 in complex with dual-acet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tv0 | ||||||
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Title | Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E | ||||||
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![]() | TRANSCRIPTION / BRD4 / bromodomain / SARS-CoV-2 / COVID / envelope protein / E protein | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Vann, K.R. / Holt, T.A. / Kutateladze, T.G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection. Authors: Vann, K.R. / Acharya, A. / Jang, S.M. / Lachance, C. / Zandian, M. / Holt, T.A. / Smith, A.L. / Pandey, K. / Durden, D.L. / El-Gamal, D. / Cote, J. / Byrareddy, S.N. / Kutateladze, T.G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163 KB | Display | ![]() |
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PDB format | ![]() | 103.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469 KB | Display | ![]() |
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Full document | ![]() | 474.7 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tuqC ![]() 3uvwS 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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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: 16355.832 Da / Num. of mol.: 4 / Fragment: BD1 (UNP residues 42-180) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1572.783 Da / Num. of mol.: 2 / Fragment: UNP residues 53-64 / Source method: obtained synthetically / Details: synthetic peptide acetylated at K53 and K63 Source: (synth.) ![]() ![]() #3: 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: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.5 M ammonium sulfate, 0.1 mM Tris, pH 8.5, 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 14, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→48.1 Å / Num. obs: 24678 / % possible obs: 96.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.116 / Rrim(I) all: 0.198 / Net I/σ(I): 5.6 / Num. measured all: 66996 / Scaling rejects: 69 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3UVW Resolution: 2.6→34.39 Å / SU ML: 0.3671 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.7033 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 25.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→34.39 Å
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Refine LS restraints |
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LS refinement shell |
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