[English] 日本語
Yorodumi- PDB-2ct5: Solution Structure of the zinc finger BED domain of the zinc fing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ct5 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1 | ||||||
Components | Zinc finger BED domain containing protein 1 | ||||||
Keywords | TRANSCRIPTION / Zinc finger BED domain containing protein 1 / dREF homolog / Putative c-like transposable element / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information protein autosumoylation / SUMO ligase activity / negative regulation by host of viral genome replication / chromatin => GO:0000785 / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / viral process / SUMOylation of chromatin organization proteins / transcription coregulator activity / PML body ...protein autosumoylation / SUMO ligase activity / negative regulation by host of viral genome replication / chromatin => GO:0000785 / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / viral process / SUMOylation of chromatin organization proteins / transcription coregulator activity / PML body / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / centrosome / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Miyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1 Authors: Miyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ct5.cif.gz | 428.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ct5.ent.gz | 355.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ct5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/2ct5 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/2ct5 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 8072.971 Da / Num. of mol.: 1 / Fragment: zinc finger BED domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZBED1X / Plasmid: P040308-29 / References: UniProt: O96006 |
---|---|
#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.09mM zinc finger BED domain U-13C, 15N; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.01mM ZNCl2; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 296 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 |