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Yorodumi- PDB-1s40: SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s40 | ||||||
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Title | SOLUTION STRUCTURE OF THE CDC13 DNA-BINDING DOMAIN COMPLEXED WITH A SINGLE-STRANDED TELOMERIC DNA 11-MER | ||||||
Components |
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Keywords | CELL CYCLE/DNA / ssDNA / single-stranded nucleic acid / recognition / specificity / cdc13 / OB-fold / telomere / CELL CYCLE-DNA COMPLEX | ||||||
Function / homology | Function and homology information CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance via telomerase ...CST complex / ribonucleoprotein complex localization / telomerase inhibitor activity / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance via telomerase / telomere maintenance / chromosome, telomeric region / cell cycle / cell division / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics | ||||||
Authors | Mitton-Fry, R.M. / Anderson, E.M. / Theobald, D.L. / Glustrom, L.W. / Wuttke, D.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13 Authors: Mitton-Fry, R.M. / Anderson, E.M. / Theobald, D.L. / Glustrom, L.W. / Wuttke, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s40.cif.gz | 681.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s40.ent.gz | 563.5 KB | Display | PDB format |
PDBx/mmJSON format | 1s40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s40 ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s40 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3476.254 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 23575.127 Da / Num. of mol.: 1 / Fragment: DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDC13, YDL220C / Production host: Escherichia coli (E. coli) / References: UniProt: P32797 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Models superimposed using Douglas Theobald's THESEUS program for multiple superpositions, variance-weighted simultaneous superpositioning. The final weighted RMSD from the mean is 0.64152A over ...Text: Models superimposed using Douglas Theobald's THESEUS program for multiple superpositions, variance-weighted simultaneous superpositioning. The final weighted RMSD from the mean is 0.64152A over all alpha-carbon atoms |
-Sample preparation
Details | Contents: 0.8-1.5mM unlabeled, 15N-labeled or 13C,15N-labeled protein; 0.9-1.7mM ssDNA; 50mM imidazole-d4, pH or pD* 7.0; 150mM NaCl; 100mM Na2SO4; 0.02% NaN3; 2mM DTT-d10 in 10% D2O/90% H2O or 100% D2O Solvent system: 10% D2O/90% H2O or 100% D2O |
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Sample conditions | Ionic strength: 150mM NaCl, 100mM Na2SO4 / pH: 7.0 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry, structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |