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Yorodumi- PDB-2epa: Solution structure of the first and second zf-C2H2 domains from h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2epa | ||||||
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Title | Solution structure of the first and second zf-C2H2 domains from human Krueppel-like factor 10 | ||||||
Components | Krueppel-like factor 10 | ||||||
Keywords | TRANSCRIPTION / Transforming growth factor-beta-inducible early growth response protein 1 / TGFB-inducible early growth response protein 1 / TIEG-1 / EGR-alpha / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information cellular response to peptide / chromatin => GO:0000785 / positive regulation of osteoclast differentiation / bone mineralization / somatic stem cell population maintenance / core promoter sequence-specific DNA binding / cellular response to starvation / regulation of circadian rhythm / circadian rhythm / sequence-specific double-stranded DNA binding ...cellular response to peptide / chromatin => GO:0000785 / positive regulation of osteoclast differentiation / bone mineralization / somatic stem cell population maintenance / core promoter sequence-specific DNA binding / cellular response to starvation / regulation of circadian rhythm / circadian rhythm / sequence-specific double-stranded DNA binding / cell-cell signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Izumi, K. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first and second zf-C2H2 domains from human Krueppel-like factor 10 Authors: Izumi, K. / Hayashi, F. / Yoshida, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2epa.cif.gz | 432.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2epa.ent.gz | 375.5 KB | Display | PDB format |
PDBx/mmJSON format | 2epa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/2epa ftp://data.pdbj.org/pub/pdb/validation_reports/ep/2epa | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8118.066 Da / Num. of mol.: 1 / Fragment: zf-C2H2, UNP residues 359-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: KLF10 / Plasmid: P060925-12 / References: UniProt: Q13118 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.46mM sample; 20mM TrisHCl(pH 7.0); 100mM NaCl; 1mM DTT; 0.02% NaN3; 0.05mM ZnCl2; 1mM IDA; 90% H2O,10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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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 |