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PDB ID: 9hro
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34972
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Name: Solution NMR structure of the synthetic tobramycin riboswitch in complex with tobramycin
Published: 2025-10-04

Title:

Solution NMR structure of the synthetic tobramycin riboswitch in complex with tobramycin

Deposition date:

2024-12-18

Original release date:

2025-10-04

Authors:

Duchardt-Ferner, E.; Woehnert, J.

Citation:

Citation: Duchardt-Ferner, E.; Kraus, L.; Limouchi, A.; Suess, B.; Wohnert, J.. "Structural basis for ligand recognition in the tobramycin riboswitch." Nucleic Acids Res. 53, .-. (2025).
PubMed: 40902004

Assembly members:

Assembly members:
entity_1, polymer, 35 residues, 11189.646 Da.
entity_TOY, non-polymer, 467.514 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGUGUUUCGGAAAGCUUCGG CUUCUACCGAGCACC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	291
15N chemical shifts	120
1H chemical shifts	360
31P chemical shifts	14

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 35 residues - 11189.646 Da.

1

G

U

G

U

C

G

2

A

G

C

U

C

G

3

C

U

C

U

A

C

G

A

4

G

C

A

C

Entity 2, unit_2 - C18 H37 N5 O9 - 467.514 Da.

1

TOY

Samples:

sample_1: RNA (35-MER) 1 ± 0.2 mM; TOBRAMYCIN 1.2 ± 0.2 mM

sample_2: RNA (35-MER), [U-100% 15N], 0.5 ± 0.2 mM; TOBRAMYCIN 0.6 ± 0.2 mM

sample_3: RNA (35-MER), [U-13C; U-15N]-Ade,Cyt, 0.75 ± 0.2 mM; TOBRAMYCIN 0.9 ± 0.2 mM

sample_4: RNA (35-MER), [U-13C; U-15N]-Ade,Cyt, 0.75 ± 0.2 mM; TOBRAMYCIN 0.9 ± 0.2 mM

sample_5: RNA (35-MER), [U-13C; U-15N]-Ura,Gua, 0.5 ± 0.2 mM; TOBRAMYCIN 0.6 ± 0.2 mM

sample_6: RNA (35-MER), [U-13C; U-15N]-Ura,Gua, 0.5 ± 0.2 mM; TOBRAMYCIN 0.6 ± 0.2 mM

sample_7: RNA (35-MER), [U-13C; U-15N], 0.84 ± 0.2 mM; TOBRAMYCIN 1.004 ± 0.2 mM

sample_8: RNA (35-MER), [U-13C; U-15N], 0.84 ± 0.2 mM; TOBRAMYCIN 1.004 ± 0.2 mM

sample_9: RNA (35-MER), [U-100% 2H], 1 ± 0.2 mM; TOBRAMYCIN 1.2 ± 0.2 mM

sample_10: RNA (35-MER), [U-100% 2H], 1 ± 0.2 mM; TOBRAMYCIN 1.2 ± 0.2 mM

sample_11: RNA (35-MER), [U-13C; U-15N]-Ura, 2.8 ± 0.2 mM; TOBRAMYCIN 2.2 ± 0.2 mM

sample_conditions_1: ionic strength: 85.9 mM; pH: 6.2; pressure: 1 bar; temperature: 283 K

sample_conditions_2: ionic strength: 85.9 mM; pH: 6.2; pressure: 1 bar; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC imino	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC amino	sample_2	isotropic	sample_conditions_1
2D HNN-COSY	sample_2	isotropic	sample_conditions_1
2D CPMG-NOESY	sample_2	isotropic	sample_conditions_1
2D long-range 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY amino	sample_2	isotropic	sample_conditions_1
2D H5(C5C4N4)H4	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_7	isotropic	sample_conditions_1
2D H1/H8-C5 HMBC	sample_5	isotropic	sample_conditions_1
2D H(N)CO	sample_5	isotropic	sample_conditions_1
2D H(C)N aromatic	sample_6	isotropic	sample_conditions_2
2D H(C)N aromatic	sample_4	isotropic	sample_conditions_2
2D H(C)N aliphatic	sample_6	isotropic	sample_conditions_2
2D H(C)N aliphatic	sample_4	isotropic	sample_conditions_2
3D 1H-13C NOESY-HSQC aro	sample_6	isotropic	sample_conditions_2
3D 1H-13C NOESY-HSQC ali	sample_6	isotropic	sample_conditions_2
3D 1H-13C NOESY-HSQC ali	sample_4	isotropic	sample_conditions_2
3D HCCH-COSY	sample_6	isotropic	sample_conditions_2
3D HCCH-COSY	sample_4	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_6	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_2
2D f1-filtered 1H-1H TOCSY	sample_7	isotropic	sample_conditions_1
2D fi1-filtered 1H-1H TOCSY	sample_8	isotropic	sample_conditions_2
2D f1,f2-filtered 1H-1H NOESY	sample_7	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_9	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_10	isotropic	sample_conditions_2
3D HCP	sample_11	isotropic	sample_conditions_2
2D H(CC)H-TOCSY	sample_4	isotropic	sample_conditions_2

Software:

TopSpin, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE NEO 600 MHz
Bruker AVANCE III HD 700 MHz
Bruker AVANCE III HD 800 MHz
Bruker AVANCE NEO 900 MHz
Bruker AVANCE III 950 MHz
Bruker AVANCE II 600 MHz

BMRB Entry 34972