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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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
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

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:

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).
PubMed: 26373429

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: in vitro transcription Host organism: E. coli - cell free

Entity Sequences (FASTA):

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
Spectrometers
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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

C

A

G

C

A

G

A

2

AP7

G

A

G

C

A

C

G

U

A

3

U

A

C

G

C

A

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