[English] 日本語
Yorodumi- PDB-2rs9: Solution structure of the bromodomain of human BRPF1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rs9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Solution structure of the bromodomain of human BRPF1 in complex with histone H4K5ac peptide | |||||||||
Components |
| |||||||||
Keywords | TRANSCRIPTION / Human BRPF1 protein / Bromodomain and PHD finger-containing protein 1 / BR140 Protein / transcription activator / Histone / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics, molecular dynamics | |||||||||
Model details | lowest energy, model 1 | |||||||||
Authors | Qin, X. / Nagashima, T. / Umehara, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: To be Published Title: Site-specific histone recognition by the bromodomain of Brpf1 and the role in MOZ/MORF histone acetyltransferase complexes Authors: Qin, X. / Hayashi, F. / Yokoyama, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rs9.cif.gz | 796.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rs9.ent.gz | 669.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rs9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rs9_validation.pdf.gz | 561.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2rs9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2rs9_validation.xml.gz | 77.5 KB | Display | |
Data in CIF | 2rs9_validation.cif.gz | 115.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/2rs9 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/2rs9 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 960.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805 |
---|---|
#2: Protein | Mass: 13777.527 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 633-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P55201 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.5 mM H4K5ac-1, 0.54 mM [U-99% 13C; U-99% 15N] Bromodomain-2, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||
Sample conditions | Ionic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 288 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics, molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 |