1LPW

Solution structure of the yeast spliceosomal U2 snRNA-intron branch site helix featuring a conserved pseudouridine


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1mM U2 snRNA-intron duplex; 10mM sodium phosphate90% H2O/10% D2O50mM sodium chloride6.4ambient278
22D NOESY1mM U2 snRNA-intron duplex; 10mM sodium phosphate100% D2O50mM sodium chloride6.4ambient293
32D TOCSY1mM U2 snRNA-intron duplex; 10mM sodium phosphate100% D2O50mM sodium chloride6.4ambient293
4DQF-COSY1mM U2 snRNA-intron duplex; 10mM sodium phosphate100% D2O50mM sodium chloride6.4ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianUNITYPLUS720
2VarianUNITYPLUS720
NMR Refinement
MethodDetailsSoftware
torsion angle molecular dynamics followed by conjugate gradient minimizationA total of 191 distance restraints were used, not including the 40 hydrogen bond distances imposed. Including the 133 dihedral restraints applied in structure calculations, 353 total restraints were applied.VNMR
NMR Ensemble Information
Conformer Selection Criterialowest energy structures that did not violate data from fluorescence experiments
Conformers Calculated Total Number800
Conformers Submitted Total Number9
Representative Model2 (lowest energy structure that agreed best with experimental data)
Additional NMR Experimental Information
DetailsThis structure was determined using standard 2D homonuclear techniques. NOESY spectra were collected at many different mixing times, so that the buildup of certain NOEs could be observed to resolve some spectral overlap.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionVNMR5.3Varian, Inc.
2data analysisSparky3.69T.D. Goddard and D.G. Kneller
3structure solutionVNMR3.851Axel Brunger
4refinementX-PLOR3.851Brunger