[English] 日本語
Yorodumi- PDB-2dmp: Solution structure of the third homeobox domain of Zinc fingers a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmp | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the third homeobox domain of Zinc fingers and homeoboxes protein 2 | ||||||
Components | Zinc fingers and homeoboxes protein 2 | ||||||
Keywords | DNA BINDING PROTEIN / homeobox domain / three helices with the DNA binding helix-turn-helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information retinal bipolar neuron differentiation / somatic stem cell population maintenance / mRNA catabolic process / negative regulation of neuron differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...retinal bipolar neuron differentiation / somatic stem cell population maintenance / mRNA catabolic process / negative regulation of neuron differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ohnishi, S. / Sasagawa, A. / 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 third homeobox domain of Zinc fingers and homeoboxes protein 2 Authors: Ohnishi, S. / Sasagawa, A. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dmp.cif.gz | 530.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dmp.ent.gz | 449.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmp_validation.pdf.gz | 342.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2dmp_full_validation.pdf.gz | 478.3 KB | Display | |
Data in XML | 2dmp_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 2dmp_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmp ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmp | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9875.972 Da / Num. of mol.: 1 / Fragment: homeobox domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZHX2 / Plasmid: P050404-24 / Production host: Cell free synthesis / References: UniProt: Q9Y6X8 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.2mM protein U-15N, 13C; 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 lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |