BMRB Entry 36263

Title:
Structure of anti-prion RNA aptamer
Deposition date:
2019-06-11
Original release date:
2020-06-30
Authors:
Mashima, T.; Lee, J.; Hayashi, T.; Nagata, T.; Kinoshita, M.; Katahira, M.
Citation:

Citation: Mashima, T.; Lee, J.; Kamatari, Y.; Hayashi, T.; Nagata, T.; Nishikawa, F.; Nishikawa, S.; Kinoshita, M.; Kuwata, K.; Katahira, M.. "Development and structural determination of an anti-PrPCaptamer that blocks pathological conformational conversion of prion protein."  Sci. Rep. 10, 4934-4934 (2020).
PubMed: 32188933

Assembly members:

Assembly members:
entity_1, polymer, 25 residues, 8441.188 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGAGGAGGAGGAAGGAGGAG GAGGA

Data sets:
Data typeCount
1H chemical shifts239

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 25 residues - 8441.188 Da.

1   GGAGGAGGAG
2   GAAGGAGGAG
3   GAGGA

Samples:

sample_1: DSS 10 uM; RNA (25-MER) 1.0 mM; potassium chloride 10 mM; potassium phosphate 10 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: DSS 10 uM; RNA (25-MER) 1.0 mM; potassium chloride 10 mM; potassium phosphate 10 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 10 mM; pH: 6.2; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 6.2; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D JR-HMBCsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-13C HSQCsample_2isotropicsample_conditions_2

Software:

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

Sparky, Goddard - chemical shift assignment, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 950 MHz