Search

NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
Authors
Bonneau, E., Legault, P.
Assembly
three-way junction from the VS ribozyme
Entity
1. RNA (47-MER) (polymer, Thiol state: not present), 47 monomers, 15180.93 Da Detail

GGACCUCCCG UCCUUGGACG GUCGAGCGAA AGCUUGUGAU UGGUCCG


2. MAGNESIUM ION (non-polymer), 24.305 × 6 Da
3. WATER (water), 18.015 × 10 Da
Total weight
15326.76 Da
Max. entity weight
15180.93 Da
Source organism
Neurospora crassa
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 89.4 %, Completeness (bb): 86.5 % Detail

Polymer type: polyribonucleotide

Total1H13C15N
All89.4 % (673 of 753)87.9 % (363 of 413)91.4 % (286 of 313)88.9 % (24 of 27)
Suger, PO486.5 % (447 of 517)84.8 % (239 of 282)88.5 % (208 of 235)
Nucleobase95.8 % (226 of 236)94.7 % (124 of 131)100.0 % (78 of 78)88.9 % (24 of 27)
Aromatic97.1 % (204 of 210)97.1 % (102 of 105)100.0 % (78 of 78)88.9 % (24 of 27)

1. RNA (47-MER)

GGACCUCCCG UCCUUGGACG GUCGAGCGAA AGCUUGUGAU UGGUCCG

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5


#NameIsotope labelingTypeConcentration
1J345-1[U-100% 15N]1.5 ~ 2.0 mM
2KClnatural abundance50 mM
3MgCl2natural abundance5 mM
4H2Onatural abundance90 %
5D2Onatural abundance10 %
Sample #2

Solvent system 100% D2O, Temperature 298 K, pH 6.5


#NameIsotope labelingTypeConcentration
6J345-2[U-100% 13C; U-100% 15N]2.0 mM
7KClnatural abundance50 mM
8MgCl2natural abundance5 mM
9D2Onatural abundance100 %
Sample #3

Solvent system 90% H2O/10% D2O, Temperature 298 K, pH 6.5


#NameIsotope labelingTypeConcentration
10J345-3[U-100% 13C; U-100% 15N]2.0 mM
11KClnatural abundance50 mM
12MgCl2natural abundance5 mM
13H2Onatural abundance90 %
14D2Onatural abundance10 %

Release date
2014-10-13
Citation
Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
Bonneau, E., Legault, P.
Biochemistry (2014), 53, 6264-6275, PubMed 25238589 , DOI 10.1021/bi500826n ,
Related entities 1. RNA (47-MER), : 1 : 1 entities Detail
Experiments performed 14 experiments Detail
NMR combined restraints 4 contents Detail
Keywords VS ribozyme, Three-way junction, Base triple, NMR, Mg2+ ions