[English] 日本語
Yorodumi- PDB-7pj1: Solution structure of isolated Drosophila histone H2A-H2B heterodimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pj1 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of isolated Drosophila histone H2A-H2B heterodimer | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / histone / H2A-H2B / dimer | ||||||
Function / homology | Function and homology information E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / polytene chromosome / nucleosome assembly / structural constituent of chromatin / nucleosome ...E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / polytene chromosome / nucleosome assembly / structural constituent of chromatin / nucleosome / chromosome / chromatin organization / protein heterodimerization activity / protein-containing complex binding / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | van Ingen, H. / Zhang, H. | ||||||
Funding support | Netherlands, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2021 Title: Mapping the electrostatic potential of the nucleosome acidic patch. Authors: Zhang, H. / Eerland, J. / Horn, V. / Schellevis, R. / van Ingen, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7pj1.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7pj1.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7pj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/7pj1 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/7pj1 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 13257.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...Gene: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865 Production host: Escherichia coli (E. coli) / References: UniProt: P84051 |
---|---|
#2: Protein | Mass: 13595.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, ...Gene: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910 Production host: Escherichia coli (E. coli) / References: UniProt: P02283 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|---|
NMR experiment | Sample state: isotropic / Type: 3D 1H-15N NOESY |
-Sample preparation
Details | Type: solution Contents: 0.5 mM histone H2A, 0.5 mM [U-15N; U-2H] histone H2B, 90% H2O/10% D2O Label: sample_1 / Solvent system: 90% H2O/10% D2O | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||
Sample conditions | Ionic strength: 300 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 bar / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 950 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: molecular dynamics / Software ordinal: 5 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 3000 / Conformers submitted total number: 20 |