[English] 日本語
Yorodumi- PDB-1wy8: Solution Structure of the N-terminal Ubiquitin-like Domain in Hum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wy8 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of the N-terminal Ubiquitin-like Domain in Human Np95/ICBP90-like Ring Finger Protein (NIRF) | ||||||
Components | Np95-like ring finger protein, isoform a | ||||||
Keywords | LIGASE / Ubiquitin-like domain / Np95/ICBP90-like ring finger (NIRF) / ubiquitin ligase / Structural genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information SUMO transferase activity / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding ...SUMO transferase activity / protein sumoylation / protein autoubiquitination / heterochromatin / pericentric heterochromatin / SUMOylation of transcription cofactors / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / regulation of cell cycle / protein ubiquitination / cell cycle / DNA binding / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Zhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the N-terminal Ubiquitin-like Domain in Human Np95/ICBP90-like Ring Finger Protein (NIRF) Authors: Zhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
| ||||||
Remark 650 | HELIX Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wy8.cif.gz | 535.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wy8.ent.gz | 450.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/1wy8 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/1wy8 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 10040.245 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free synthesis / Gene: UHRF2 / Plasmid: P041101-10 / References: UniProt: Q96PU4 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.91mM protein U-15N, 13C/20mM d-Tris-HCl, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |