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Yorodumi- PDB-2d9g: Solution structure of the zf-RanBP domain of YY1-associated factor 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d9g | ||||||
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Title | Solution structure of the zf-RanBP domain of YY1-associated factor 2 | ||||||
Components | YY1-associated factor 2 | ||||||
Keywords | TRANSCRIPTION / zf-RanBP domain / YY1-associated factor 2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of G0 to G1 transition / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / transcription coregulator activity / transcription corepressor activity / transcription coactivator activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding ...negative regulation of G0 to G1 transition / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / transcription coregulator activity / transcription corepressor activity / transcription coactivator activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Zhang, H.P. / Izumi, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the zf-RanBP domain of YY1-associated factor 2 Authors: Zhang, H.P. / Izumi, K. / 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 | 2d9g.cif.gz | 293.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d9g.ent.gz | 244.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d9g_validation.pdf.gz | 345.3 KB | Display | wwPDB validaton report |
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Full document | 2d9g_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 2d9g_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2d9g_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/2d9g ftp://data.pdbj.org/pub/pdb/validation_reports/d9/2d9g | 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: 5590.167 Da / Num. of mol.: 1 / Fragment: zf-RanBP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: YAF2 / Plasmid: P050322-12 / References: UniProt: Q8IY57 |
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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: 1.05mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 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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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 |