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NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma
Authors
Kruschel, D., Skilandat, M., Sigel, R.K. O.
Assembly
d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma
Entity
1. d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma (polymer, Thiol state: not present), 29 monomers, 9364.517 Da Detail

GGAGUAUGUA UUGGCACUGA GCAUACUCC


Formula weight
9364.517 Da
Source organism
Saccharomyces cerevisiae
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 68.5 %, Completeness (bb): 59.2 % Detail

Polymer type: polyribonucleotide

Total1H13C15N
All68.5 % (317 of 463)81.3 % (205 of 252)52.3 % (102 of 195)62.5 % (10 of 16)
Suger, PO459.2 % (189 of 319)77.6 % (135 of 174)37.2 % (54 of 145)
Nucleobase88.9 % (128 of 144)89.7 % (70 of 78)96.0 % (48 of 50)62.5 % (10 of 16)
Aromatic90.9 % (120 of 132)93.9 % (62 of 66)96.0 % (48 of 50)62.5 % (10 of 16)

1. RNA (29-MER)

GGAGUAUGUA UUGGCACUGA GCAUACUCC

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K


#NameIsotope labelingTypeConcentration
1RNA (29-MER)natural abundance0.4 ~ 1.2 mM
2potassium chloridenatural abundance10 mM
3EDTAnatural abundance10 uM
4D2Onatural abundance100 %
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K


#NameIsotope labelingTypeConcentration
5RNA (29-MER)natural abundance0.4 ~ 1.2 mM
6potassium chloridenatural abundance10 mM
7EDTAnatural abundance10 uM
8D2Onatural abundance10 %
9H2Onatural abundance90 %
Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K


#NameIsotope labelingTypeConcentration
10RNA (29-MER)[U-100% 13C; U-100% 15N]0.7 mM
11potassium chloridenatural abundance10 mM
12EDTAnatural abundance10 uM
13D2Onatural abundance10 %
14H2Onatural abundance90 %
Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K


#NameIsotope labelingTypeConcentration
15RNA (29-MER)[U-100% 13C; U-100% 15N]0.7 mM
16potassium chloridenatural abundance10 mM
17EDTAnatural abundance10 uM
18Pf1 phagenatural abundance25.6 mg/mL
19D2Onatural abundance10 %
20H2Onatural abundance90 %
Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K


#NameIsotope labelingTypeConcentration
21RNA (29-MER)[U-100% 13C; U-100% 15N]0.7 mM
22potassium chloridenatural abundance10 mM
23EDTAnatural abundance10 uM
24D2Onatural abundance100 %
Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K


#NameIsotope labelingTypeConcentration
25RNA (29-MER)[3',4',5',5'',5, 100% 2H]0.6 mM
26potassium chloridenatural abundance10 mM
27EDTAnatural abundance10 uM
28D2Onatural abundance100 %

Release date
2013-12-15
Citation
NMR structure of the 5' splice site in the group IIB intron Sc.ai5γ--conformational requirements for exon-intron recognition
Kruschel, D., Skilandat, M., Sigel, R.K.O.
RNA (2014), 20, 295-307, PubMed 24448450 , DOI 10.1261/rna.041137.113 ,
Related entities 1. d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma, : 1 : 2 entities Detail
Experiments performed 15 experiments Detail
NMR combined restraints 8 contents Detail
Keywords EBS1, group II intron, hairpin, ribozyme, RNA, splicing