+Open data
-Basic information
Entry | Database: PDB / ID: 1v63 | ||||||
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Title | Solution structure of the 6th HMG box of mouse UBF1 | ||||||
Components | Nucleolar transcription factor 1 | ||||||
Keywords | DNA BINDING PROTEIN / Transcription factor / DNA binding / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / positive regulation of transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I ...RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RNA polymerase I cis-regulatory region sequence-specific DNA binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / positive regulation of transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / cellular response to leukemia inhibitory factor / fibrillar center / scaffold protein binding / chromatin binding / nucleolus / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Sato, M. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the 6th HMG box of mouse UBF1 Authors: Sato, M. / Saito, K. / Koshiba, S. / Inoue, M. / 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 | 1v63.cif.gz | 632.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v63.ent.gz | 529.3 KB | Display | PDB format |
PDBx/mmJSON format | 1v63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/1v63 ftp://data.pdbj.org/pub/pdb/validation_reports/v6/1v63 | 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: 11610.073 Da / Num. of mol.: 1 / Fragment: HMG box domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1300010N03 / Plasmid: P030107-54 / References: UniProt: P25976 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.2mM HMG box domain U-15N,13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-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 |