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- PDB-1s2f: Average solution structure of a pseudo-5'-splice site from the ne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s2f | ||||||||||||||||||||
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Title | Average solution structure of a pseudo-5'-splice site from the negative regulator of splicing of Rous Sarcoma virus | ||||||||||||||||||||
![]() | 5'-R(*![]() RNA / NRS / U1 snRNP binding site / 5' splice site | Function / homology | RNA / RNA (> 10) | ![]() Method | SOLUTION NMR / Simulated annealing. Torsion angle dynamics in refinement. | Model type details | minimized average | ![]() Cabello-Villegas, J. / Giles, K.E. / Soto, A.M. / Yu, P. / Beemon, K.L. / Wang, Y.X. | ![]() ![]() Title: Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor. Authors: Cabello-Villegas, J. / Giles, K.E. / Soto, A.M. / Yu, P. / Mougin, A. / Beemon, K.L. / Wang, Y.X. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.7 KB | Display | ![]() |
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PDB format | ![]() | 15.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 292.4 KB | Display | ![]() |
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Full document | ![]() | 292.2 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 3.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 7350.335 Da / Num. of mol.: 1 / Fragment: Pseudo 5'-splice site / Source method: obtained synthetically / Details: In vitro transcription |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Exchangeable proton spectra collected at 15 Celsius |
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Sample preparation
Details | Contents: RNA Residues 907-929 from NRS (NRS23) / Solvent system: 10 mM Sodium Phosphate, 25 mM NaCl, pH 6.5 |
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Sample conditions | Ionic strength: 25 mM NaCl, 10 mM NaPi / pH: 6.5 / 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 |
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Processing
NMR software |
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Refinement | Method: Simulated annealing. Torsion angle dynamics in refinement. Software ordinal: 1 Details: 100 structurews were calculated, the minimized average from the 15 lowest energy structures is presented. Constraints used: 423 distance, 63 torsion angle, 117 orientation (RDC). The DELPIC ...Details: 100 structurews were calculated, the minimized average from the 15 lowest energy structures is presented. Constraints used: 423 distance, 63 torsion angle, 117 orientation (RDC). The DELPIC database was employed in the refinement as follows: torsion angle database active for all residues, base-base positional database active for residues 907-912, 914-916, and 921-929. DELPHIC database reference: Clore, G.M. Kuszewski, J. J. Am. Chem. Soc. 125: 1518-1525 | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |