BMRB Entry 19698

Title:
Solution NMR structure of a preQ1 Class II riboswitch from Streptococcus pneumoniae   PubMed: 24469808
Deposition date:
2013-12-20
Original release date:
2014-01-27
Authors:
Kang, Mijeong; Eichhorn, Catherine; Feigon, Juli
Citation:

Citation: Kang, Mijeong; Eichhorn, Catherine; Feigon, Juli. "Structural determinants for ligand capture by a class II preQ1 riboswitch."  Proc. Natl. Acad. Sci. U.S.A. 111, E663-E671 (2014).

Assembly members:

Assembly members:
RNA_(59-MER), polymer, 59 residues, 18903.389 Da.
7-DEAZA-7-AMINOMETHYL-GUANINE, non-polymer, 179.179 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: enzymatic semisynthesis

Experimental source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: enzymatic semisynthesis

Entity Sequences (FASTA):

Data sets:
Data typeCount
13C chemical shifts399
15N chemical shifts20
1H chemical shifts620

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA (59-MER)1
27-DEAZA-7-AMINOMETHYL-GUANINE2

Entities:

Entity 1, RNA (59-MER) 59 residues - 18903.389 Da.

1   GCUUGGUGCU
2   UAGCUUCUUU
3   CACCAAGCAU
4   AUUACACGCG
5   GAUAACCGCC
6   AAAGGAGAA

Entity 2, 7-DEAZA-7-AMINOMETHYL-GUANINE - 179.179 Da.

1   PRF

Samples:

sample_1: RNA (59-MER)1.0 – 1.2 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; potassium chloride 60 mM; calcium chloride 3 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_2: RNA (59-MER)1.0 – 1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_3: RNA (59-MER), [U-50% 2H, 0.8 – 1.0 mM; potassium chloride 60 mM; calcium Chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_4: RNA (59-MER), [U-13C; U-15N]-Ade, 1.0 – 1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_5: RNA (59-MER), [U-13C; U-15N]-Gua, 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_6: RNA (59-MER), [U-13C; U-15N]-Cyt, 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_7: RNA (59-MER), [U-13C; U-15N]-Ura, 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; D2O, [U-100% 2H], 100%

sample_8: RNA (59-MER), [U-100% 13C; U-100% 15N], 1~1.2 mM; potassium chloride 60 mM; calcium chloride 3 mM; 7-DEAZA-7-AMINOMETHYL-GUANINE 2 mM; H2O 90%; D2O, [U-100% 2H], 10%

sample_conditions_1: ionic strength: 66 mM; pH: 6.15; pressure: 1 atm; temperature: 300 K

sample_conditions_2: ionic strength: 66 mM; pH: 6.15; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_2
3D HCCH-TOCSYsample_5isotropicsample_conditions_2
3D HCCH-TOCSYsample_6isotropicsample_conditions_2
3D HCCH-TOCSYsample_7isotropicsample_conditions_2
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_8isotropicsample_conditions_1
2D 1H-15N HSQCsample_8isotropicsample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, data analysis

xwinnmr, Bruker Biospin - collection, processing

TOPSPIN, Bruker Biospin - collection, processing

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMRDraw, Johnson, One Moon Scientific - peak picking

InsightII, Accelrys Software Inc. - data analysis

NMR spectrometers:

  • Bruker DRX 600 MHz
  • Bruker Avance 800 MHz