2L8F

Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA90% H2O/10% D2O0.16.5ambient273
22D 1H-13C HSQC1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA90% H2O/10% D2O0.16.5ambient273
32D 1H-13C HSQC1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA90% H2O/10% D2O0.15ambient273
42D 1H-13C HSQC1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient293
52D 1H-1H NOESY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA90% H2O/10% D2O0.16.5ambient273
62D 1H-1H NOESY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA90% H2O/10% D2O0.16.5ambient273
72D 1H-1H NOESY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA90% H2O/10% D2O0.16.5ambient293
82D 1H-1H NOESY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient293
92D 1H-1H NOESY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient273
102D 1H-1H TOCSY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient293
112D 1H-1H TOCSY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient273
122D 1H-1H COSY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient293
132D 31P-1H COSY1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10100% D2O0.16.5ambient293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA500
2VarianINOVA600
NMR Refinement
MethodDetailsSoftware
simulated annealingNMRPipe
NMR Ensemble Information
Conformer Selection Criteriano restraint violations; low constraint energy
Conformers Calculated Total Number40
Conformers Submitted Total Number10
Representative Model1 (lowest constraint energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2chemical shift assignmentSparky3.114Goddard
3data analysisSparky3.114Goddard
4structure solutionAmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
5collectionVNMR6.1CVarian
6structure solutionCNS1.2Brunger, Adams, Clore, Gros, Nilges and Read
7refinementAmber