[English] 日本語
Yorodumi- PDB-2co9: Solution structure of the HMG_box domain of thymus high mobility ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2co9 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the HMG_box domain of thymus high mobility group box protein TOX from mouse | ||||||
Components | thymus high mobility group box protein TOX | ||||||
Keywords | TRANSCRIPTION / Tox protein / HMG box domain / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information NK T cell lineage commitment / regulation of positive thymic T cell selection / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / leukocyte differentiation / positive regulation of natural killer cell differentiation / CD8-positive, alpha-beta T cell lineage commitment / cerebral cortex neuron differentiation / CD4-positive, alpha-beta T cell lineage commitment / positive regulation of DNA demethylation / natural killer cell differentiation ...NK T cell lineage commitment / regulation of positive thymic T cell selection / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / leukocyte differentiation / positive regulation of natural killer cell differentiation / CD8-positive, alpha-beta T cell lineage commitment / cerebral cortex neuron differentiation / CD4-positive, alpha-beta T cell lineage commitment / positive regulation of DNA demethylation / natural killer cell differentiation / lymphocyte differentiation / Peyer's patch development / positive regulation of neural precursor cell proliferation / lymph node development / positive regulation of neuron projection development / chromatin DNA binding / chromatin organization / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, H. / 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 HMG_box domain of thymus high mobility group box protein TOX from mouse Authors: Li, H. / 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 | 2co9.cif.gz | 605.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2co9.ent.gz | 526.2 KB | Display | PDB format |
PDBx/mmJSON format | 2co9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/2co9 ftp://data.pdbj.org/pub/pdb/validation_reports/co/2co9 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 11054.450 Da / Num. of mol.: 1 / Fragment: HMG box Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Tox / Plasmid: P040719-05 / References: UniProt: Q8R4H0, UniProt: Q66JW3*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.28mM HMG_box domain U-13C, 15N; 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 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 |