Solution structure of branaplam bound to the RNA duplex formed upon 5'-splice site recognition
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.001 M unlabled RNA duplex, 0.001 M unlabled Branaplam, 0.01 M unlabled MES, 0.05 M unlabled NaCl | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVANCE III HD 900 |
| 2 | 2D 1H-13C HSQC aliphatic | 0.001 M unlabled RNA duplex, 0.001 M unlabled Branaplam, 0.01 M unlabled MES, 0.05 M unlabled NaCl | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVANCE III HD 900 |
| 3 | 2D 1H-13C HSQC aromatic | 0.001 M unlabled RNA duplex, 0.001 M unlabled Branaplam, 0.01 M unlabled MES, 0.05 M unlabled NaCl | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVANCE III HD 900 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III HD | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | AmberTools | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | AmberTools | 2023 | Case D |
| 2 | structure calculation | CYANA | 3 | Guntert, Mumenthaler and Wuthrich |
| 3 | chemical shift assignment | CARA | Keller and Wuthrich | |
| 4 | peak picking | CYANA | Guntert, Mumenthaler and Wuthrich | |
