[English] 日本語
Yorodumi- PDB-2dod: Solution structure of the first FF domain of human transcription ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dod | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the first FF domain of human transcription factor CA150 | ||||||
Components | Transcription elongation regulator 1 | ||||||
Keywords | TRANSCRIPTION / FF domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity ...transcription elongation factor activity / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / mRNA processing / transcription corepressor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dyanamics, simulated annealing | ||||||
Authors | Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first FF domain of human transcription factor CA150 Authors: Suzuki, S. / Muto, Y. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
| ||||||
Remark 650 | HELIX Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dod.cif.gz | 515.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dod.ent.gz | 434.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/2dod ftp://data.pdbj.org/pub/pdb/validation_reports/do/2dod | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9430.725 Da / Num. of mol.: 1 / Fragment: FF domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TCERG1, CA150, TAF2S / Plasmid: P051128-07 / Production host: Cell free synthesis / References: UniProt: O14776 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||
NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.2mM 13C/15N-PROTEIN; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dyanamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |