BMRB Entry 25526

Name: Re-refined solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostamycin complex
Published: 2016-02-01

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PDB ID: 2n0j
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25526
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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: Re-refined solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostamycin complex PubMed: 26661511

Deposition date: 2015-03-09 Original release date: 2016-02-01

Authors: Duchardt-Ferner, Elke; Gottstein-Schmidtke, Sina; Weigand, Julia; Ohlenschlaeger, Oliver; Wurm, Jan-Philip; Hammann, Christian; Suess, Beatrix; Woehnert, Jens

Citation: Elke, Duchardt-Ferner; Julia, Weigand; Oliver, Ohlenschlaeger; Sina, Schmidtke; Beatrix, Suess; Jens, Woehnert. "What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch" Angew. Chem. Int. Ed. 55, 1527-1530 (2016).

Assembly members:
RNA_(27-MER), polymer, 27 residues, 8557.091 Da.
RIBOSTAMYCIN, non-polymer, 454.473 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: reverse transcriptase

Entity Sequences (FASTA):
RNA_(27-MER): GGCUGCUUGUCCUUUAAUGG UCCAGUC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	180
15N chemical shifts	27
1H chemical shifts	205
31P chemical shifts	8

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	RIBOSTAMYCIN	2

Entities:

Entity 1, entity_1 27 residues - 8557.091 Da.

1

G

C

U

G

C

U

G

U

2

C

U

A

U

G

3

U

C

A

G

U

C

Entity 2, RIBOSTAMYCIN - C17 H34 N4 O10 - 454.473 Da.

1

RIO

Samples:

sample_1: entity_1 0.8 mM; potassium phosphate 25 mM; potassium chloride 50 mM; H2O 90%; D2O 10%

sample_2: entity_1, [U-100% 15N], 0.8 mM; RIBOSTAMYCIN 0.9 mM; potassium phosphate 25 mM; potassium chloride 50 mM; H2O 90%; D2O 10%

sample_3: entity_1, [U-100% 13C; U-100% 15N], 1.1 mM; RIBOSTAMYCIN 1.2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; D2O 100%

sample_4: entity_1, [U-13C; U-15N; U-2H], 1.1 mM; RIBOSTAMYCIN 1.2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; D2O 100%

sample_5: entity_1, [U-100% 13C; U-100% 15N], 1.1 mM; RIBOSTAMYCIN 1.2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; H2O 90%; D2O 10%

sample_6: entity_1, [U-13C; U-15N; U-2H], 1.1 mM; RIBOSTAMYCIN 1.2 mM; potassium phosphate 25 mM; potassium chloride 50 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.2; temperature: 282.5 K

sample_conditions_2: pH: 6.2; temperature: 283 K

sample_conditions_3: pH: 6.2; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_3
3D HNCO	sample_5	isotropic	sample_conditions_2
3D H(CCO)NH	sample_5	isotropic	sample_conditions_2
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_3
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_4	isotropic	sample_conditions_3
2D DQF-COSY	sample_4	isotropic	sample_conditions_3
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_3
2D 1H-1H TOCSY	sample_6	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_6	isotropic	sample_conditions_2

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA v1.8.4.2, Wuthrich - chemical shift assignment, peak picking

SPARKY, Goddard - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 800 MHz
Bruker Avance 900 MHz
Bruker Avance 950 MHz