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Yorodumi- PDB-7to9: BRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7to9 | ||||||
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Title | BRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE) | ||||||
Components |
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Keywords | TRANSCRIPTION / BET / bromodomain / RaPID / BRD3 / acetylated | ||||||
Function / homology | Function and homology information lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mackay, J.P. / Low, J.K.K. / Patel, K. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome. Authors: Low, J.K.K. / Patel, K. / Jones, N. / Solomon, P. / Norman, A. / Maxwell, J.W.C. / Pachl, P. / Matthews, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Walport, L.J. / Mackay, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7to9.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7to9.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 7to9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7to9_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 7to9_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | 7to9_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 7to9_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/7to9 ftp://data.pdbj.org/pub/pdb/validation_reports/to/7to9 | HTTPS FTP |
-Related structure data
Related structure data | 7to7C 7to8C 7toaC 3s91S S: Starting model for refinement C: citing same article (ref.) |
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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: 15095.392 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059 #2: Protein/peptide | | Mass: 2267.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #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: 2.05 Å3/Da / Density % sol: 40.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES, pH 7.5, 0.2 M sodium chloride, 10% v/v 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953732 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.5 Å / Num. obs: 35429 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 22.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.039 / Rrim(I) all: 0.062 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1763 / CC1/2: 0.785 / Rpim(I) all: 0.41 / Rrim(I) all: 0.878 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3S91 Resolution: 1.6→40.5 Å / SU ML: 0.2231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.477 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: 29.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40.5 Å
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Refine LS restraints |
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LS refinement shell |
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