BMRB Entry 27794

Name: 1H, 13C, and 15N chemical shift assignments of the GTP 9-12 RNA aptamer in complex with GTP
Published: 2019-04-29

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR27794

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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 the GTP 9-12 RNA aptamer in complex with GTP

Deposition date:

2019-02-20

Original release date:

2019-04-29

Authors:

Wolter, Antje; Pianu, Angela; Kremser, Johannes; Strebitzer, Elisabeth; Kreutz, Christoph; Duchardt-Ferner, Elke; Woehnert, Jens

Citation:

Citation: Wolter, Antje; Pianu, Angela; Kremser, Johannes; Strebitzer, Elisabeth; Schnieders, Robbin; Fuertig, Boris; Kreutz, Christoph; Duchardt-Ferner, Elke; Woehnert, Jens. "NMR resonance assignments for the GTP-binding RNA aptamer 9-12 in complex with GTP" Biomol. NMR Assignments ., .-. (2019).
PubMed: 31030336

Assembly members:

Assembly members:
GTP_9-12_aptamer, polymer, 39 residues, Formula weight is not available
entity_GTP, non-polymer, 523.180 Da.
entity_MG, 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: Escherichia coli, cell free Vector: pSP64

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GTP_9-12_aptamer: GGGAGCAGUUCAGGUAACCA CGUAAGAUACGGUGCUCCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	324
15N chemical shifts	146
1H chemical shifts	351

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1
2	ligand	2
3	Mg	3

Entities:

Entity 1, RNA 39 residues - Formula weight is not available

1

G

A

G

C

A

G

U

2

C

A

G

U

A

C

A

3

C

G

U

A

G

A

U

A

C

4

G

U

G

C

U

C

Entity 2, ligand - C10 H16 N5 O14 P3 - 523.180 Da.

1

GTP

Entity 3, Mg - Mg - 24.305 Da.

1

MG

Samples:

unlabeled_H2O: GTP 9-12 aptamer 0.86 mM; nucleoside triphosphate GTP 1.29 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

unlabeled_GTP-13C15N_H2O: GTP 9-12 aptamer 0.86 mM; nucleoside triphosphate GTP, [U-13C; U-15N], 1.29 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; H2O 95%; D2O 5%

unlabeled_GTP-13C15N_D2O: GTP 9-12 aptamer 0.86 mM; nucleoside triphosphate GTP, [U-13C; U-15N], 1.29 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

15N_H2O: GTP 9-12 aptamer, [U-15N], 1.035 mM; nucleoside triphosphate GTP, [U-15N], 1.55 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 5%; H2O 95%

13C15N-A-C_H2O: GTP 9-12 aptamer, [U-13C; U-15N]-Ade/Cyt, 1.24 mM; nucleoside triphosphate GTP 1.86 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 5%; H2O 95%

13C15N-A-C_D2O: GTP 9-12 aptamer, [U-13C; U-15N]-Ade/Cyt, 1.24 mM; nucleoside triphosphate GTP 1.86 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

13C15N-G-U_H2O: GTP 9-12 aptamer, [U-13C; U-15N]-Ade/Cyt, 1.13 mM; nucleoside triphosphate GTP 1.7 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 5%; H2O 95%

13C15N-G-U_D2O: GTP 9-12 aptamer, [U-13C; U-15N]-Ade/Cyt, 1.13 mM; nucleoside triphosphate GTP 1.7 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 100%

13C15N_H2O: GTP 9-12 aptamer, [U-13C; U-15N], 0.67 mM; nucleoside triphosphate GTP 1.34 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 5%; H2O 95%

sel_2H_H2O: GTP 9-12 aptamer, [U-2H], 1 mM; nucleoside triphosphate GTP, [U-2H], 1.5 mM; magnesium acetate 2.5 mM; potassium chloride 25 mM; potassium phosphate 25 mM; D2O 5%; H2O 95%

sample_conditions_1: ionic strength: 50 mM; pH: 6.3; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.3; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	15N_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC	13C15N-G-U_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	15N_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	13C15N-A-C_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	13C15N-G-U_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	13C15N_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	13C15N-A-C_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	13C15N-G-U_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	13C15N-A-C_D2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	13C15N-G-U_D2O	isotropic	sample_conditions_1
3D HCCH-TOCSY	13C15N-A-C_D2O	isotropic	sample_conditions_1
3D HCCH-TOCSY	13C15N-G-U_D2O	isotropic	sample_conditions_1
3D HCCH-COSY	13C15N-A-C_D2O	isotropic	sample_conditions_1
3D HCCH-COSY	13C15N-G-U_D2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	unlabeled_H2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sel_2H_H2O	isotropic	sample_conditions_2
3D 1H-13C NOESY aromatic	13C15N-A-C_H2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	13C15N-G-U_H2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	13C15N-A-C_D2O	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	13C15N-G-U_D2O	isotropic	sample_conditions_1
3D 1H-15N NOESY	15N_H2O	isotropic	sample_conditions_1
2D 1H-13C H(N)CO	13C15N-G-U_H2O	isotropic	sample_conditions_1
HNN-COSY	15N_H2O	isotropic	sample_conditions_1
SELLR HNN-COSY	15N_H2O	isotropic	sample_conditions_1
amino HNN-COSY	15N_H2O	isotropic	sample_conditions_1
2D lr-1H-13C-HSQC	13C15N-G-U_H2O	isotropic	sample_conditions_1
2D H(C)N aromatic	13C15N-A-C_D2O	isotropic	sample_conditions_1
2D H(C)N aromatic	13C15N-G-U_D2O	isotropic	sample_conditions_1
2D H(C)N aliphatic	13C15N-A-C_D2O	isotropic	sample_conditions_1
2D H(C)N aliphatic	13C15N-G-U_D2O	isotropic	sample_conditions_1
2D H5(C5C4N3)H3	13C15N-G-U_H2O	isotropic	sample_conditions_1
2D H5(C5C4N4)H4	13C15N-A-C_H2O	isotropic	sample_conditions_1
TROSY relayed HCCH COSY	13C15N-A-C_D2O	isotropic	sample_conditions_1
2D 13C-15N HSQC	13C15N_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC	unlabeled_GTP-13C15N_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC NH2 only	unlabeled_GTP-13C15N_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	unlabeled_GTP-13C15N_H2O	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	unlabeled_GTP-13C15N_D2O	isotropic	sample_conditions_1
2D 1H-13C-NOESY aromatic	unlabeled_GTP-13C15N_H2O	isotropic	sample_conditions_1
2D 1H-13C-NOESY aliphatic	unlabeled_GTP-13C15N_H2O	isotropic	sample_conditions_1
2D HCCH-TOCSY	13C15N-A-C_D2O	isotropic	sample_conditions_1
2D CPMG-NOESY	15N_H2O	isotropic	sample_conditions_1
2D 1H-15N HSQC	15N_H2O	isotropic	sample_conditions_2
2D 1H-15N HSQC NH2 only	15N_H2O	isotropic	sample_conditions_2
2D 1H-1H NOESY	unlabeled_H2O	isotropic	sample_conditions_2
2D lr-1H-15N-HSQC	15N_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 3.5, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker Avance 950 MHz
Bruker Avance 800 MHz
Bruker Avance 700 MHz
Bruker Avance 600 MHz