BMRB Entry 25661

Name: 1H, 13C, and 15N chemical shift assignments of a the GTP class II RNA aptamer in complex with GTP
Published: 2016-09-15

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PDB ID: 5lwj
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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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
13C chemical shifts	265
15N chemical shifts	117
1H chemical shifts	307
31P chemical shifts	7

Additional metadata:

Assembly
Samples and Experiments
Software
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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

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

Biological Magnetic Resonance Data Bank

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

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