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Basic information

Entry
Database: PDB / ID: 2mi0
TitleNMR structure of the I-V kissing-loop interaction of the Neurospora VS ribozyme
Components
  • 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'
  • 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'
KeywordsRNA / Neurospora VS ribozyme / kissing-loop interaction / substrate recognition / U-turn / NMR structural studies
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNeurospora (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsBouchard, P. / Legault, P.
CitationJournal: Biochemistry / Year: 2014
Title: Structural insights into substrate recognition by the neurospora varkud satellite ribozyme: importance of u-turns at the kissing-loop junction.
Authors: Bouchard, P. / Legault, P.
History
DepositionDec 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 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'
B: 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 500structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 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'


Mass: 7049.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Neurospora (fungus)
#2: RNA chain 5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'


Mass: 6721.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Neurospora (fungus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-15N HSQC
1312D 1H-15N HSQC NH2 only
1432D 1H-15N HSQC NH2 only
1512D 1H-15N NHH COSY
1632D 1H-15N NHH COSY
1772D 1H-15N HMQC J=21Hz
1882D 1H-15N HMQC J=21Hz
2912D 1H-15N CPMG NOESY
21032D 1H-15N CPMG NOESY
11132D 1H-1H flip-back WATERGATE NOESY
11213D 15N-edited NOESY-HSQC
11333D 15N-edited NOESY-HSQC
11422D 1H-13C CT-HSQC
11542D 1H-13C CT-HSQC
11652D 1H-13C CT-HSQC
11762D 1H-13C CT-HSQC
11893D 15N/13C-edited NOESY-HSQC
119103D 15N/13C-edited NOESY-HSQC
12023D 13C-edited HMQC-NOESY
12143D 13C-edited HMQC-NOESY
12253D 13C-edited HMQC-NOESY
12363D 13C-edited HMQC-NOESY
12423D (H)CCH-COSY
12543D (H)CCH-COSY
12663D (H)CCH-COSY
12711D 15N-decoupled 1H WATERGATE
12831D 15N-decoupled 1H WATERGATE
12911D 15N-filtered 1H WATERGATE
13031D 15N-filtered 1H WATERGATE
13111D 15N-edited 1H WATERGATE
13231D 15N-edited 1H WATERGATE
133112D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3-2.2 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 chloride, 90% H2O/10% D2O90% H2O/10% D2O
21.5 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 chloride, 100% D2O100% D2O
31.4 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 chloride, 90% H2O/10% D2O90% H2O/10% D2O
41.7 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 chloride, 100% D2O100% D2O
51.4 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 chloride, 100% D2O100% D2O
61.4 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 chloride, 100% D2O100% D2O
71.4 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 chloride, 100% D2O100% D2O
81.3 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 chloride, 100% D2O100% D2O
91.7 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 chloride, 90% H2O/10% D2O90% H2O/10% D2O
101.5 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 chloride, 90% H2O/10% D2O90% H2O/10% D2O
110.2-0.3 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 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-11.3-2.21
mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-2[U-15N]1.3-2.21
10 mMTris-3[U-2H]1
50 mMsodium chloride-41
0.05 mMsodium azide-51
5 mMmagnesium chloride-61
1.5 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-72
1.5 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-8[U-13C; U-15N]2
10 mMTris-9[U-2H]2
50 mMsodium chloride-102
0.05 mMsodium azide-112
5 mMmagnesium chloride-122
1.4 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-13[U-15N]3
1.4 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-143
10 mMTris-15[U-2H]3
50 mMsodium chloride-163
0.05 mMsodium azide-173
5 mMmagnesium chloride-183
1.7 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-19[U-13C; U-15N]4
1.7 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-204
10 mMTris-21[U-2H]4
50 mMsodium chloride-224
0.05 mMsodium azide-234
5 mMmagnesium chloride-244
1.4 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-25[U-13C; U-15N]-Gua5
1.4 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-265
10 mMTris-27[U-2H]5
50 mMsodium chloride-285
0.05 mMsodium azide-295
5 mMmagnesium chloride-305
1.4 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-31[U-13C; U-15N]-Gua6
1.4 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-326
10 mMTris-33[U-2H]6
50 mMsodium chloride-346
0.05 mMsodium azide-356
5 mMmagnesium chloride-366
1.4 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-37[U-15N]7
1.4 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-387
10 mMTris-39[U-2H]7
50 mMsodium chloride-407
0.05 mMsodium azide-417
5 mMmagnesium chloride-427
1.3 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-438
1.3 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-44[U-15N]8
10 mMTris-45[U-2H]8
50 mMsodium chloride-468
0.05 mMsodium azide-478
5 mMmagnesium chloride-488
1.7 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-49[U-13C; U-15N]9
1.7 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-509
10 mMTris-51[U-2H]9
50 mMsodium chloride-529
0.05 mMsodium azide-539
5 mMmagnesium chloride-549
1.5 mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-5510
1.5 mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-56[U-13C; U-15N]10
10 mMTris-57[U-2H]10
50 mMsodium chloride-5810
0.05 mMsodium azide-5910
5 mMmagnesium chloride-6010
mM5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3'-61[U-15N]0.2-0.311
mM5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'-62[U-15N]0.2-0.311
10 mMTris-63[U-2H]11
50 mMsodium chloride-6411
0.05 mMsodium azide-6511
5 mMmagnesium chloride-6611
mg/mLPf1 phage-6714.6-20.511
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM NaCl, 5 mM MgCl2 7.0 ambient 298 K
250 mM NaCl, 5 mM MgCl2 7.0 ambient 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
PyMOLSchrodingerstructure analysis
PyMOLSchrodingerstructure display
CCPNMR_suiteCCPNchemical shift assignment
CCPNMR_suiteCCPNdata analysis
CCPNMR_suiteCCPNpeak picking
Curves+(CURVES) Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K.structure analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 21

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