BMRB Entry 36263

Name: Structure of anti-prion RNA aptamer
Published: 2020-06-30

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PDB ID: 6k84
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36263
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	239

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 25 residues - 8441.188 Da.

1

G

A

G

A

G

A

G

2

G

A

G

A

G

A

G

3

G

A

G

A

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:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D JR-HMBC	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_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