2RU7

Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-1, 1 mM P16-2, 10 mM potassium phosphate-3, 10 mM potassium chloride-4, 0.01 mM DSS-5, 3 mM sodium azide-695% H2O/5% D2O106.2ambient atm278
22D 1H-1H NOESY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-1, 1 mM P16-2, 10 mM potassium phosphate-3, 10 mM potassium chloride-4, 0.01 mM DSS-5, 3 mM sodium azide-695% H2O/5% D2O106.2ambient atm303
32D 1H-1H NOESY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 mM P16-8, 10 mM potassium phosphate-9, 10 mM potassium chloride-10, 0.01 mM DSS-11, 3 mM sodium azide-12100% D2O106.2ambient atm278
42D 1H-1H NOESY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 mM P16-8, 10 mM potassium phosphate-9, 10 mM potassium chloride-10, 0.01 mM DSS-11, 3 mM sodium azide-12100% D2O106.2ambient atm303
52D 1H-1H TOCSY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-1, 1 mM P16-2, 10 mM potassium phosphate-3, 10 mM potassium chloride-4, 0.01 mM DSS-5, 3 mM sodium azide-695% H2O/5% D2O106.2ambient atm303
62D 1H-1H TOCSY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 mM P16-8, 10 mM potassium phosphate-9, 10 mM potassium chloride-10, 0.01 mM DSS-11, 3 mM sodium azide-12100% D2O106.2ambient atm303
72D DQF-COSY1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 mM P16-8, 10 mM potassium phosphate-9, 10 mM potassium chloride-10, 0.01 mM DSS-11, 3 mM sodium azide-12100% D2O106.2ambient atm303
82D 1H-13C HSQC1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 mM P16-8, 10 mM potassium phosphate-9, 10 mM potassium chloride-10, 0.01 mM DSS-11, 3 mM sodium azide-12100% D2O106.2ambient atm303
9JRHMBC1 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-1, 1 mM P16-2, 10 mM potassium phosphate-3, 10 mM potassium chloride-4, 0.01 mM DSS-5, 3 mM sodium azide-695% H2O/5% D2O106.2ambient atm303
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX600
2BrukerDRX600
NMR Refinement
MethodDetailsSoftware
energy minimization, simulated annealingXwinNMR
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number10
Conformers Submitted Total Number5
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionXwinNMRBruker Biospin
2collectionTopSpinBruker Biospin
3processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4chemical shift assignmentSparkyGoddard
5peak pickingSparkyGoddard
6data analysisTALOSCornilescu, Delaglio and Bax
7structure solutionX-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clore
8refinementX-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clore
9refinementAmber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman