BMRBj - BMREntryMaster

Found 1 Document (0.237 seconds)

BMRB: 36263

Structure of anti-prion RNA aptamer

Authors

Mashima, T., Lee, J.H., Hayashi, T., Nagata, T., Kinoshita, M., Katahira, M.

Assembly

RNA (25-MER)

Entity

1. RNA (25-MER) (polymer, Thiol state: not present), 25 monomers, 8504.158 Da Detail

GGAGGAGGAG GAAGGAGGAG GAGGA

Formula weight

8504.158 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 100.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	100.0 % (200 of 200)	100.0 % (200 of 200)
Suger, PO4	100.0 % (150 of 150)	100.0 % (150 of 150)
Nucleobase	100.0 % (50 of 50)	100.0 % (50 of 50)
Aromatic	100.0 % (50 of 50)	100.0 % (50 of 50)

1. entity 1

GGAGGAGGAG GAAGGAGGAG GAGGA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2, Details 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		10 uM
2	RNA (25-MER)	natural abundance	RNA	1.0 mM
3	potassium chloride	natural abundance		10 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance	solvent	95 %
6	D2O	[U-2H]	solvent	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2, Details 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		10 uM
8	RNA (25-MER)	natural abundance	RNA	1.0 mM
9	potassium chloride	natural abundance	salt	10 mM
10	potassium phosphate	natural abundance	buffer	10 mM
11	D2O	[U-2H]	solvent	100 %

Release date

2020-05-13

Citation

Development and structural determination of an anti-PrP^C aptamer that blocks pathological conformational conversion of prion protein
Mashima, T., Lee, J.H., Kamatari, Y.O., Hayashi, T., Nagata, T., Nishikawa, F., Nishikawa, S., Kinoshita, M., Kuwata, K., Katahira, M.
Sci. Rep. (2020), 10, 4934-4934, PubMed 32188933 , DOI 10.1038/s41598-020-61966-4 , Abstract

Experiments performed 6 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2, Details 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		10 uM
2	RNA (25-MER)	natural abundance	RNA	1.0 mM
3	potassium chloride	natural abundance		10 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance	solvent	95 %
6	D2O	[U-2H]	solvent	5 %

2 2D JR-HMBC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.2, Details 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	DSS	natural abundance		10 uM
2	RNA (25-MER)	natural abundance	RNA	1.0 mM
3	potassium chloride	natural abundance		10 mM
4	potassium phosphate	natural abundance		10 mM
5	H2O	natural abundance	solvent	95 %
6	D2O	[U-2H]	solvent	5 %

3 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 288 K, pH 6.2, Details 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS, 100% D2O

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		10 uM
8	RNA (25-MER)	natural abundance	RNA	1.0 mM
9	potassium chloride	natural abundance	salt	10 mM
10	potassium phosphate	natural abundance	buffer	10 mM
11	D2O	[U-2H]	solvent	100 %

4 2D DQF-COSY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		10 uM
8	RNA (25-MER)	natural abundance	RNA	1.0 mM
9	potassium chloride	natural abundance	salt	10 mM
10	potassium phosphate	natural abundance	buffer	10 mM
11	D2O	[U-2H]	solvent	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		10 uM
8	RNA (25-MER)	natural abundance	RNA	1.0 mM
9	potassium chloride	natural abundance	salt	10 mM
10	potassium phosphate	natural abundance	buffer	10 mM
11	D2O	[U-2H]	solvent	100 %

6 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
7	DSS	natural abundance		10 uM
8	RNA (25-MER)	natural abundance	RNA	1.0 mM
9	potassium chloride	natural abundance	salt	10 mM
10	potassium phosphate	natural abundance	buffer	10 mM
11	D2O	[U-2H]	solvent	100 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr36263_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr36263_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	239		100.0 (chain: 1, length: 25)
1	Chemical shift references	chem_shift_reference_1	OK	1		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 25, Sequence coverage: 100.0%

--------10--------20-----
GGAGGAGGAGGAAGGAGGAGGAGGA
|||||||||||||||||||||||||
GGAGGAGGAGGAAGGAGGAGGAGGA

Total number of assignments
- ¹H chemical shifts: 239

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	H21	9.043
1	G	H22	10.333
2	G	H21	6.303
2	G	H22	9.07
3	A	H61	6.373
3	A	H62	8.355
4	G	H21	6.566
4	G	H22	10.045
5	G	H21	5.762
5	G	H22	9.89
7	G	H21	9.032
7	G	H22	10.22
8	G	H21	6.727
8	G	H22	9.481
9	A	H61	6.433
9	A	H62	8.377
10	G	H22	9.411
11	G	H21	5.843
11	G	H22	9.206
14	G	H21	9.021
14	G	H22	10.3
15	G	H21	6.345
15	G	H22	9.121
16	A	H61	6.363
16	A	H62	8.384
17	G	H21	6.584
17	G	H22	10.037
18	G	H21	5.786
18	G	H22	9.968
20	G	H21	8.954
20	G	H22	10.225
21	G	H21	6.279
21	G	H22	9.525
22	A	H61	6.375
22	A	H62	8.508
23	G	H21	5.965
23	G	H22	8.959
24	G	H21	5.489
24	G	H22	9.37

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	200	200	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	150	150	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	34	100.0

Histogram of normalized assigned chemical shifts

Keywords Aptamer, Quadruplex, RNA

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Found 1 Document (0.237 seconds)

BMRB: 36263

Sample #1

Sample #2

Experiments performed 6 experiments Detail

Instrument

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Sample

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Chemical shift validation 3 contents Detail