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Solution structure of the HIV-1 frameshift inducing stem-loop RNA
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
1 mM HIV-1 frameshift inducing stem-loop RNA
90% H2O/10% D2O, or 99.99% D2O
50 mM
6.8
ambient
303
2
2D TOCSY
1 mM HIV-1 frameshift inducing stem-loop RNA
90% H2O/10% D2O, or 99.99% D2O
50 mM
6.8
ambient
303
3
3D_13C-separated_NOESY
1 mM HIV-1 frameshift inducing stem-loop RNA
90% H2O/10% D2O, or 99.99% D2O
50 mM
6.8
ambient
303
4
2D HNN-COSY
1 mM HIV-1 frameshift inducing stem-loop RNA
90% H2O/10% D2O, or 99.99% D2O
50 mM
6.8
ambient
298
5
2D NOESY
1 mM HIV-1 frameshift inducing stem-loop RNA
90% H2O/10% D2O, or 99.99% D2O
50 mM
6.8
ambient
283
6
2D 1H-13C HSQC
1 mM HIV-1 frameshift inducing stem-loop RNA
90% H2O/10% D2O, or 99.99% D2O
50 mM
6.8
ambient
303
NMR Refinement
Method
Details
Software
torsion angle molecular dynamics, Cartesian space simulated annealing and molecular dynamics, residual dipolar coupling
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees
Conformers Calculated Total Number
100
Conformers Submitted Total Number
20
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
The incorporation of residual dipolar couplings and the direct detection of hydrogen bonds with HNN-COSY were used in solving this structure