2MI0 | pdb_00002mi0

NMR structure of the I-V kissing-loop interaction of the Neurospora VS ribozyme


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N HSQC1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
22D 1H-15N HSQC1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
32D 1H-15N HSQC NH2 only1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
42D 1H-15N HSQC NH2 only1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
52D 1H-15N NHH COSY1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
62D 1H-15N NHH COSY1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
72D 1H-15N HMQC J=21Hz1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
82D 1H-15N HMQC J=21Hz1.3 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
92D 1H-15N CPMG NOESY1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient288
102D 1H-15N CPMG NOESY1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient288
112D 1H-1H flip-back WATERGATE NOESY1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
123D 15N-edited NOESY-HSQC1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
133D 15N-edited NOESY-HSQC1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
142D 1H-13C CT-HSQC1.5 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.5 mM [U-13C; U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
152D 1H-13C CT-HSQC1.7 mM [U-13C; U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.7 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
162D 1H-13C CT-HSQC1.4 mM [U-13C; U-15N]-Gua 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
172D 1H-13C CT-HSQC1.4 mM [U-13C; U-15N]-Gua 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
183D 15N/13C-edited NOESY-HSQC1.7 mM [U-13C; U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.7 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
193D 15N/13C-edited NOESY-HSQC1.5 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.5 mM [U-13C; U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
203D 13C-edited HMQC-NOESY1.5 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.5 mM [U-13C; U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
213D 13C-edited HMQC-NOESY1.7 mM [U-13C; U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.7 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
223D 13C-edited HMQC-NOESY1.4 mM [U-13C; U-15N]-Gua 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
233D 13C-edited HMQC-NOESY1.4 mM [U-13C; U-15N]-Gua 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
243D HCCH-COSY1.5 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.5 mM [U-13C; U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
253D HCCH-COSY1.7 mM [U-13C; U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.7 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
263D HCCH-COSY1.4 mM [U-13C; U-15N]-Gua 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride100% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
271D 15N-decoupled 1H WATERGATE1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
281D 15N-decoupled 1H WATERGATE1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
291D 15N-filtered 1H WATERGATE1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
301D 15N-filtered 1H WATERGATE1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
311D 15N-edited 1H WATERGATE1.3-2.2 mM 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.3-2.2 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
321D 15N-edited 1H WATERGATE1.4 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 1.4 mM 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
332D 1H-15N HSQC0.2-0.3 mM [U-15N] 5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3', 0.2-0.3 mM [U-15N] 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3', 10 mM [U-2H] Tris, 50 mM sodium chloride, 0.05 mM sodium azide, 5 mM magnesium chloride, 14.6-20.5 mg/mL Pf1 phage90% H2O/10% D2O50 mM NaCl, 5 mM MgCl27.0ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianINOVA500
2VarianINOVA600
NMR Refinement
MethodDetailsSoftware
simulated annealingNMRPipe
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number500
Conformers Submitted Total Number21
Representative Model1 (minimized average structure)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2processingNMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3refinementX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
4structure solutionX-PLOR NIHSchwieters, Kuszewski, Tjandra and Clore
5structure analysisPyMOLSchrodinger
6structure displayPyMOLSchrodinger
7chemical shift assignmentCCPNMR_suiteCCPN
8data analysisCCPNMR_suiteCCPN
9peak pickingCCPNMR_suiteCCPN
10structure analysisCurves+(CURVES) Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K.