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Yorodumi- PDB-2din: Solution structure of the Myb_DNA-binding domain of human Cell di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2din | ||||||
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Title | Solution structure of the Myb_DNA-binding domain of human Cell division cycle 5-like protein | ||||||
Components | Cell division cycle 5-like protein | ||||||
Keywords | DNA BINDING PROTEIN / Myb_DNA-binding domain / Cell cycle / DNA binding / Spliceosome / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Prp19 complex / U2-type catalytic step 2 spliceosome / WD40-repeat domain binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / DNA damage checkpoint signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / mRNA splicing, via spliceosome / DNA-binding transcription activator activity, RNA polymerase II-specific ...Prp19 complex / U2-type catalytic step 2 spliceosome / WD40-repeat domain binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / DNA damage checkpoint signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / mRNA splicing, via spliceosome / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / DNA repair / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Yoneyama, M. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the Myb_DNA-binding domain of human Cell division cycle 5-like protein Authors: Yoneyama, M. / Tochio, N. / 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 | 2din.cif.gz | 393.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2din.ent.gz | 331.9 KB | Display | PDB format |
PDBx/mmJSON format | 2din.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/2din ftp://data.pdbj.org/pub/pdb/validation_reports/di/2din | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7297.183 Da / Num. of mol.: 1 / Fragment: Myb_DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: CDC5L / Plasmid: P050905-03 / References: UniProt: Q99459 |
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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: 1.13mM Myb_DNA-binding domain U-15N, 13C; 20mM d-Tris HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 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: target function, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |