[English] 日本語
Yorodumi- PDB-2ep8: Solution structure of the BRCT domain from human Pescadillo homolog 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ep8 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the BRCT domain from human Pescadillo homolog 1 | ||||||
Components | Pescadillo homolog 1 | ||||||
Keywords | CELL CYCLE / a/b/a 3 layers / nucleolus / ribosome biogenesis / DNA damage / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA processing / chromosome / cell population proliferation ...PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA processing / chromosome / cell population proliferation / regulation of cell cycle / nucleolus / RNA binding / nucleoplasm / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the BRCT domain from human Pescadillo homolog 1 Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ep8.cif.gz | 610.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ep8.ent.gz | 510.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ep8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ep8_validation.pdf.gz | 338.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ep8_full_validation.pdf.gz | 474.9 KB | Display | |
Data in XML | 2ep8_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 2ep8_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/2ep8 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/2ep8 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 11237.758 Da / Num. of mol.: 1 / Fragment: BRCT domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PES1 / Plasmid: P060821-06 / References: UniProt: O00541 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.46mM uniformly 13C,15N-labeled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 10% D2O, 90% H2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 900 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |