[English] 日本語
Yorodumi- PDB-2el5: Solution structure of the 18th zf-C2H2 domain from human Zinc fin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2el5 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the 18th zf-C2H2 domain from human Zinc finger protein 268 | ||||||
Components | Zinc finger protein 268 | ||||||
Keywords | TRANSCRIPTION / Alternative splicing / DNA-binding / Metal-binding / Nuclear protein / Transcription regulation / Zinc / Zinc-finger / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / positive regulation of protein homodimerization activity / Generic Transcription Pathway / regulation of mitotic cell cycle / positive regulation of cell differentiation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation ...: / positive regulation of protein homodimerization activity / Generic Transcription Pathway / regulation of mitotic cell cycle / positive regulation of cell differentiation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / regulation of cell cycle / positive regulation of cell migration / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the 18th zf-C2H2 domain from human Zinc finger protein 268 Authors: Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2el5.cif.gz | 228.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2el5.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 2el5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/2el5 ftp://data.pdbj.org/pub/pdb/validation_reports/el/2el5 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 4346.562 Da / Num. of mol.: 1 / Fragment: zf-C2H2 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: ZNF268 / Plasmid: P061218-18 / References: UniProt: Q14587 |
---|---|
#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.08mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 50uM ZnCl2; 1mM IDA; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |