BMRB Entry 30942

Name: An RNA aptamer that decreases flavin redox potential
Published: 2022-07-13

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PDB ID: 7rwr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30942
MolProbity Validation Chart

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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:

An RNA aptamer that decreases flavin redox potential

Deposition date:

2021-08-20

Original release date:

2022-07-13

Authors:

Gremminger, T.; Li, J.; Chen, S.; Heng, X.

Citation:

Citation: Samuelian, John; Gremminger, Thomas; Song, Zhenwei; Poudyal, Raghav; Li, Jun; Zhou, Yuanzhe; Staller, Seth; Carballo, Johan; Roychowdhury-Saha, Manami; Chen, Shi-Jie; Burke, Donald; Heng, Xiao; Baum, Dana. "An RNA aptamer that shifts the reduction potential of metabolic cofactors" Nat. Chem. Biol. 18, 1263-1269 (2022).
PubMed: 36097297

Assembly members:

Assembly members:
entity_1, polymer, 38 residues, 12234.317 Da.
entity_FMN, non-polymer, 456.344 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGAUACACAAGAGUGAUUGA AACUAAGUCUGUGUAUCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	165

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 38 residues - 12234.317 Da.

1

G

A

U

A

C

A

C

A

2

G

A

G

U

G

A

U

G

A

3

A

C

U

A

G

U

C

U

4

G

U

G

U

A

U

C

Entity 2, unit_2 - C17 H21 N4 O9 P - 456.344 Da.

1

FMN

Samples:

sample_1: RNA (38-MER), [U-1H], 300 uM; FMN, [U-1H], 300 uM; MgCl2 20 mM

sample_2: RNA (38-MER), [A-H, C-D, G-H, U-D], 300 uM; FMN, [U-1H], 300 uM; MgCl2 20 mM

sample_3: RNA (38-MER), [A-H, C-H, G-D, U-D], 300 uM; FMN, [U-1H], 300 uM; MgCl2 20 mM

sample_4: RNA (38-MER), [A-D, C-D, G-H, U-H], 300 uM; FMN, [U-H], 300 uM; MgCl2 20 mM

sample_5: RNA (38-MER), [A-8D, C-H, G-H, U-5,6D2], 300 uM; FMN, [U-1H], 300 uM; MgCl2 20 mM

sample_6: RNA (38-MER), [U-100% 13C; U-100% 15N], 300 uM; FMN, [U-1H], 300 uM; MgCl2 20 mM

sample_7: RNA (38-MER), [U-100% 13C; U-100% 15N], 300 uM; FMN, [dioxopyrimidine-13C4, 15N2], 300 uM; MgCl2 20 mM

sample_conditions_1: ionic strength: 20 mM; pH: 7.5; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 283 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 NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
HNN-COSY	sample_6	isotropic	sample_conditions_2
F1fF2f-NOESY	sample_6	isotropic	sample_conditions_1
F2f-NOESY	sample_6	isotropic	sample_conditions_1
HNN-COSY	sample_7	isotropic	sample_conditions_2

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRViewJ, Johnson - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure calculation

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

NMR spectrometers:

Bruker AVANCE 800 MHz