BMRB Entry 17106

Name: solution structure of a preQ1 riboswitch (Class I) aptamer bound to preQ1
Published: 2010-08-19

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PDB ID: 2l1v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17106
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: solution structure of a preQ1 riboswitch (Class I) aptamer bound to preQ1 PubMed: 19285444

Deposition date: 2010-08-06 Original release date: 2010-08-19

Authors: Kang, Mijeong; Zhang, Qi; Feigon, Juli

Citation: Kang, Mijeong; Zhang, Qi; Peterson, Robert; Feigon, Juli. "Structural Insights into Riboswitch Control of the Biosynthesis of Queuosine, a Modified Nucleotide Found in the Anticodon of tRNA" Mol. Cell 33, 784-790 (2009).

Assembly members:
RNA_(36-MER), polymer, 36 residues, 11527.992 Da.
PRF, non-polymer, 179.179 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: enzymatic semisynthesis

Entity Sequences (FASTA):
RNA_(36-MER): GGAGAGGUUCUAGUUAUACC CUCUAUAAAAAACUAA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	229
15N chemical shifts	67
1H chemical shifts	319

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (36-MER)	1
2	7-DEAZA-7-AMINOMETHYL-GUANINE	2

Entities:

Entity 1, RNA (36-MER) 36 residues - 11527.992 Da.

1

G

A

G

A

G

U

C

2

U

A

G

U

A

U

A

C

3

C

U

C

U

A

U

A

4

A

C

U

A

Entity 2, 7-DEAZA-7-AMINOMETHYL-GUANINE - C7 H9 N5 O - 179.179 Da.

1

PRF

Samples:

sample_1: preQ1-RNA 36mer, [U-13C; U-15N]-Cyt, 1 mM; D2O 100%; KCl 50 mM

sample_2: preQ1-RNA 36mer 1 mM; H2O 90%; D2O 10%; KCl 50 mM

sample_3: preQ1-RNA 36mer, [U-13C; U-15N], 0.7 mM; H2O 90%; D2O 10%; KCl 50 mM

sample_4: preQ1-RNA 36mer, [U-13C; U-15N]-Ade, 1 mM; D2O 100%; KCl 50 mM

sample_5: preQ1-RNA 36mer, [U-13C; U-15N]-Gua, 1 mM; D2O 100%; KCl 50 mM

sample_6: preQ1-RNA 36mer, [U-13C; U-15N]-Ura, 1 mM; D2O 100%; KCl 50 mM

sample_7: preQ1-RNA 36mer, U-H5,3',4',5',5''-2H, 1 mM; D2O 100%; KCl 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.3; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N COSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1

Software:

xwinnmr, Varian - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Bruker DRX 500 MHz
Bruker DRX 600 MHz
Bruker Avance 800 MHz