BMRB Entry 30942

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:
Data typeCount
1H chemical shifts165

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 38 residues - 12234.317 Da.

1   GGAUACACAA
2   GAGUGAUUGA
3   AACUAAGUCU
4   GUGUAUCC

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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_5isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
HNN-COSYsample_6isotropicsample_conditions_2
F1fF2f-NOESYsample_6isotropicsample_conditions_1
F2f-NOESYsample_6isotropicsample_conditions_1
HNN-COSYsample_7isotropicsample_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