BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25661

Title: 1H, 13C, and 15N chemical shift assignments of a the GTP class II RNA aptamer in complex with GTP   PubMed: 26373429

Authors: Wolter, Antje; Duchardt-Ferner, Elke; Nasiri, Amir; Wunderlich, Christoph; Kreutz, Christoph; Woehnert, Jens

Citation: Wolter, Antje; Duchardt-Ferner, Elke; Nasiri, Amir; Hantke, Katharina; Wunderlich, Christoph; Kreutz, Christoph; Woehnert, Jens. "NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP"  Biomol. NMR Assign. 10, 101-105 (2016).

Assembly members:
GTP_class_II_aptamer, polymer, 34 residues, Formula weight is not available
N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE, non-polymer, 348.229 Da.
GUANOSINE-5'-TRIPHOSPHATE, non-polymer, 523.180 Da.
MAGNESIUM ION, non-polymer, 24.305 Da.

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: in vitro transcription   Host organism: E. coli - cell free

Entity Sequences (FASTA):
GTP_class_II_aptamer: GGCAGCCAGAXGAGCACGUA UACGCAAGGCUGUC

Data sets:
Data typeCount
13C chemical shifts265
15N chemical shifts117
1H chemical shifts307
31P chemical shifts7

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1RNA1
2N1-Protonated Adenosine-5'-Monophosphate2
3nucleoside triphosphate GTP3
4Mg4

Entities:

Entity 1, RNA 34 residues - Formula weight is not available

X (AP7) represents the protonated A11

1   GGCAGCCAGA
2   AP7GAGCACGUA
3   UACGCAAGGC
4   UGUC

Entity 2, N1-Protonated Adenosine-5'-Monophosphate - C10 H15 N5 O7 P - 348.229 Da.

1   AP7

Entity 3, nucleoside triphosphate GTP - C10 H16 N5 O14 P3 - 523.180 Da.

1   GTP

Entity 4, Mg - Mg - 24.305 Da.

1   MG

Samples:

1_RNAunl_H2O: GTP class II aptamer 0.66 mM; GTP, [U-13C; U-15N], 1.32 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

2_RNAunl_D2O: GTP class II aptamer 0.66 mM; GTP, [U-13C; U-15N], 1.32 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

3_RNAunl_H2O_2: GTP class II aptamer 0.9 mM; GTP, [U-13C; U-15N], 1.8 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

4_15NRNA: GTP class II aptamer, [U-15N], 0.33 mM; GTP, [U-13C; U-15N], 0.5 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

5_13C15NRNA_H2O: GTP class II aptamer, [U-13C; U-15N], 0.36 mM; GTP 0.72 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 90%; D2O 10%

6_13C15NRNA_D2O: GTP class II aptamer, [U-13C; U-15N], 1.2 mM; GTP 2.4 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

7_Ade_H2O: GTP class II aptamer, [U-13C; U-15N]-Ade, 1.1 mM; GTP, [U-13C; U-15N], 2.2 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

8_Ade_D2O: GTP class II aptamer, [U-13C; U-15N]-Ade, 1.1 mM; GTP, [U-13C; U-15N], 2.2 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

9_Cyt_H2O: GTP class II aptamer, [U-13C; U-15N]-Cyt, 0.73 mM; GTP, [U-15N], 1.46 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

10_Cyt_D2O: GTP class II aptamer, [U-13C; U-15N]-Cyt, 0.73 mM; GTP, [U-15N], 1.46 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

11_GU_H2O: GTP class II aptamer, [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura, 0.82 mM; GTP 1.64 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

12_GU_D2O: GTP class II aptamer, [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura, 0.82 mM; GTP, [U-15N], 1.64 mM; magnesium acetate 2 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

sample_conditions_1: pH: 6.3; pressure: 1 atm; temperature: 293 K

sample_conditions_2: pH: 6.3; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
1D 1H-HS11ECHO1_RNAunl_H2Oisotropicsample_conditions_1
2D 1H-1H NOESY1_RNAunl_H2Oisotropicsample_conditions_1
2D 1H-15N HSQC1_RNAunl_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic2_RNAunl_D2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromatic1_RNAunl_H2Oisotropicsample_conditions_1
2D 1H-15N HSQC7_Ade_H2Oisotropicsample_conditions_1
2D 1H-15N HSQC NH2 only7_Ade_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromatic7_Ade_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic8_Ade_D2Oisotropicsample_conditions_1
2D 1H-15N HSQC11_GU_H2Oisotropicsample_conditions_1
2D 1H-15N HSQC NH2 only11_GU_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromatic11_GU_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic12_GU_D2Oisotropicsample_conditions_1
2D 1H-15N HSQC NH2 only9_Cyt_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aromatic9_Cyt_H2Oisotropicsample_conditions_1
2D 1H-13C HSQC aliphatic10_Cyt_D2Oisotropicsample_conditions_1
3D HCCH-TOCSY8_Ade_D2Oisotropicsample_conditions_1
3D HCCH-TOCSY12_GU_D2Oisotropicsample_conditions_1
3D HCCH-TOCSY10_Cyt_D2Oisotropicsample_conditions_1
3D HCCH-COSY8_Ade_D2Oisotropicsample_conditions_1
3D HCCH-COSY12_GU_D2Oisotropicsample_conditions_1
3D HCCH-COSY10_Cyt_D2Oisotropicsample_conditions_1
2D 1H-15N HNN-COSY4_15NRNAisotropicsample_conditions_2
2D 1H-13C HNCO11_GU_H2Oisotropicsample_conditions_1
2D 1H-13C H5(6)C5(6)C4NH311_GU_H2Oisotropicsample_conditions_1
2D 1H-13C H5(6)C5(6)C4N4H49_Cyt_H2Oisotropicsample_conditions_1
2D 1H-15N HCN aromatic8_Ade_D2Oisotropicsample_conditions_1
2D 1H-15N HCN aromatic12_GU_D2Oisotropicsample_conditions_1
2D 1H-15N HCN aromatic10_Cyt_D2Oisotropicsample_conditions_1
2D 1H-15N HCN aliphatic8_Ade_D2Oisotropicsample_conditions_1
2D 1H-15N HCN aliphatic12_GU_D2Oisotropicsample_conditions_1
2D 1H-15N HCN aliphatic12_GU_D2Oisotropicsample_conditions_1
2D 1H-1H HCCH-TOCSY (adenine)8_Ade_D2Oisotropicsample_conditions_1
2D 1H-15N 2bond-HSQC4_15NRNAisotropicsample_conditions_2
2D 1H-31P H(C)P8_Ade_D2Oisotropicsample_conditions_1
2D 1H-31P H(C)P12_GU_D2Oisotropicsample_conditions_1
2D 1H-31P H(C)P10_Cyt_D2Oisotropicsample_conditions_1
2D 1H-1H-H8(C8CN1)H111_GU_H2Oisotropicsample_conditions_1
2D HCCH-COSY2_RNAunl_D2Oisotropicsample_conditions_1
2D 1H-13C long-rangeH8(C8)C5(N1)H111_GU_H2Oisotropicsample_conditions_1

Software:

CARA v1.8.4.2., Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

TOPSPIN v2.1 to 3.2, Bruker Biospin - processing

NMR spectrometers:

  • Bruker Avance 950 MHz
  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 700 MHz
  • Bruker Avance 600 MHz

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