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Yorodumi- PDB-2ebl: Solution structure of the Zinc finger, C4-type domain of human CO... -
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-Basic information
Entry | Database: PDB / ID: 2ebl | ||||||
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Title | Solution structure of the Zinc finger, C4-type domain of human COUP transcription factor 1 | ||||||
Components | COUP transcription factor 1 | ||||||
Keywords | TRANSCRIPTION / DNA-binding / Metal-binding / Nuclear protein / Receptor / Transcription regulation / Zinc / EAR3 / ERBAL3 / TFCOUP1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information anatomical structure development / retinoic acid-responsive element binding / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / sequence-specific double-stranded DNA binding / negative regulation of neuron projection development / sequence-specific DNA binding / transcription coactivator activity ...anatomical structure development / retinoic acid-responsive element binding / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / sequence-specific double-stranded DNA binding / negative regulation of neuron projection development / sequence-specific DNA binding / transcription coactivator activity / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Koshiba, S. / Watabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the Zinc finger, C4-type domain of human COUP transcription factor 1 Authors: Yoneyama, M. / Koshiba, S. / Watabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ebl.cif.gz | 529.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ebl.ent.gz | 440 KB | Display | PDB format |
PDBx/mmJSON format | 2ebl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ebl_validation.pdf.gz | 343.5 KB | Display | wwPDB validaton report |
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Full document | 2ebl_full_validation.pdf.gz | 476 KB | Display | |
Data in XML | 2ebl_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 2ebl_validation.cif.gz | 50.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/2ebl ftp://data.pdbj.org/pub/pdb/validation_reports/eb/2ebl | HTTPS FTP |
-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: 9900.315 Da / Num. of mol.: 1 / Fragment: Zinc finger, C4-type Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: NR2F1, EAR3, ERBAL3, TFCOUP1 / Plasmid: P051212-03 / References: UniProt: P10589 |
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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: 1.22mM Zinc finger, C4-type domain U-15N,13C; 20mM d-Tris HCl (pH 7.0); 100mM NaCl; 1mM d-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: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / 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,target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |