BMRB Entry 25661
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25661
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Title: 1H, 13C, and 15N chemical shift assignments of a the GTP class II RNA aptamer in complex with GTP PubMed: 26373429
Deposition date: 2015-06-15 Original release date: 2016-09-15
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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 265 |
| 15N chemical shifts | 117 |
| 1H chemical shifts | 307 |
| 31P chemical shifts | 7 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | RNA | 1 |
| 2 | N1-Protonated Adenosine-5'-Monophosphate | 2 |
| 3 | nucleoside triphosphate GTP | 3 |
| 4 | Mg | 4 |
Entities:
Entity 1, RNA 34 residues - Formula weight is not available
X (AP7) represents the protonated A11
| 1 | G | G | C | A | G | C | C | A | G | A | ||||
| 2 | AP7 | G | A | G | C | A | C | G | U | A | ||||
| 3 | U | A | C | G | C | A | A | G | G | C | ||||
| 4 | U | G | U | C |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 1D 1H-HS11ECHO | 1_RNAunl_H2O | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | 1_RNAunl_H2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 1_RNAunl_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | 2_RNAunl_D2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | 1_RNAunl_H2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 7_Ade_H2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC NH2 only | 7_Ade_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | 7_Ade_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | 11_GU_H2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC NH2 only | 11_GU_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | 11_GU_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | 12_GU_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC NH2 only | 9_Cyt_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aromatic | 9_Cyt_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | 10_Cyt_D2O | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | 12_GU_D2O | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | 10_Cyt_D2O | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | 12_GU_D2O | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | 10_Cyt_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HNN-COSY | 4_15NRNA | isotropic | sample_conditions_2 |
| 2D 1H-13C HNCO | 11_GU_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C H5(6)C5(6)C4NH3 | 11_GU_H2O | isotropic | sample_conditions_1 |
| 2D 1H-13C H5(6)C5(6)C4N4H4 | 9_Cyt_H2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HCN aromatic | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HCN aromatic | 12_GU_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HCN aromatic | 10_Cyt_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HCN aliphatic | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HCN aliphatic | 12_GU_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N HCN aliphatic | 12_GU_D2O | isotropic | sample_conditions_1 |
| 2D 1H-1H HCCH-TOCSY (adenine) | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 2D 1H-15N 2bond-HSQC | 4_15NRNA | isotropic | sample_conditions_2 |
| 2D 1H-31P H(C)P | 8_Ade_D2O | isotropic | sample_conditions_1 |
| 2D 1H-31P H(C)P | 12_GU_D2O | isotropic | sample_conditions_1 |
| 2D 1H-31P H(C)P | 10_Cyt_D2O | isotropic | sample_conditions_1 |
| 2D 1H-1H-H8(C8CN1)H1 | 11_GU_H2O | isotropic | sample_conditions_1 |
| 2D HCCH-COSY | 2_RNAunl_D2O | isotropic | sample_conditions_1 |
| 2D 1H-13C long-rangeH8(C8)C5(N1)H1 | 11_GU_H2O | isotropic | sample_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