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Yorodumi- PDB-2ely: Solution structure of the third zf-C2H2 domain from human Zinc fi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ely | ||||||
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Title | Solution structure of the third zf-C2H2 domain from human Zinc finger protein 224 | ||||||
Components | Zinc finger protein 224 | ||||||
Keywords | TRANSCRIPTION / DNA-binding / Metal-binding / Nuclear protein / Phosphorylation / Polymorphism / Repressor / 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 Generic Transcription Pathway / transcription repressor complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...Generic Transcription Pathway / transcription repressor complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR | ||||||
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 third zf-C2H2 domain from human Zinc finger protein 224 Authors: Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ely.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ely.ent.gz | 211.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ely.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ely_validation.pdf.gz | 339.9 KB | Display | wwPDB validaton report |
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Full document | 2ely_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 2ely_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2ely_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/2ely ftp://data.pdbj.org/pub/pdb/validation_reports/el/2ely | 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/peptide | Mass: 4681.192 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: ZNF224 / Plasmid: P061225-19 / References: UniProt: Q9NZL3 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.19mM 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 |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 700 MHz |
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-Processing
NMR software |
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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 |