7QA2
Solution structure of an intramolecular RNA G-quadruplex formed by the 6A mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.6 mM BCL-2 6A | 90% H2O/10% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
2 | 2D 1H-1H NOESY | 0.6 mM BCL-2 6A | 100% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
3 | 2D 1H-1H TOCSY | 0.6 mM BCL-2 6A | 100% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
4 | 2D 1H-13C HSQC | 0.6 mM BCL-2 6A | 100% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
5 | JR-HMBC | 0.6 mM BCL-2 6A | 90% H2O/10% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 600 |
6 | H8N2 HNN-COSY | 0.15 mM [U-13C; U-15N]-Gua BCL-2 6A | 90% H2O/10% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
7 | H1N2 HNN-COSY | 0.15 mM [U-13C; U-15N]-Gua BCL-2 6A | 90% H2O/10% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
8 | constant-time HSQC | 0.4 mM [U-13C; U-15N]-Ade BCL-2 6A | 100% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 600 |
9 | constant-time HSQC | 0.15 mM [U-13C; U-15N]-Gua BCL-2 6A | 100% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
10 | constant-time HSQC | 0.4 mM [U-13C; U-15N]-Ura BCL-2 6A | 100% D2O | 2 mM | 7.0 | 1 atm | 298 | Bruker AVANCE 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 4.0.6 | Bruker Biospin |
2 | chemical shift assignment | NMRFAM-SPARKY | 1.414 | Lee W, Tonelli M, Markley JL |
3 | peak picking | NMRFAM-SPARKY | 1.414 | Lee W, Tonelli M, Markley JL |
4 | structure calculation | X-PLOR NIH | 3.0 | Schwieters, Kuszewski, Tjandra and Clore |
5 | refinement | X-PLOR NIH | 3.0 | Schwieters, Kuszewski, Tjandra and Clore |