BMRBj - BMREntryMaster

Found 1 Document (0.733 seconds)

BMRB: 11489

2RU7

RNA aptamer against prion protein in complex with the partial binding peptide

Authors

Mashima, T., Nishikawa, F., Kamatari, Y.O., Fujiwara, H., Nishikawa, S., Kuwata, K., Katahira, M.

Assembly

RNA aptamer against prion protein

Entity

1. RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3') (polymer, Thiol state: not present), 12 monomers, 4096.484 × 2 Da Detail

GGAGGAGGAG GA

2. P16 (polymer, Thiol state: not present), 12 monomers, 1384.537 × 2 Da Detail

GQWNKPSKPK TN

Total weight

10962.042 Da

Max. entity weight

4096.484 Da

Source organism

Bos taurus

Exptl. method

solution NMR

Refine. method

energy minimization, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.6 %, Completeness (bb): 88.4 % Detail

Polymer type: polyribonucleotide polypeptide(L)

	Total	¹H
All	85.6 % (155 of 181)	85.6 % (155 of 181)
Backbone	88.4 % (84 of 95)	88.4 % (84 of 95)
Sidechain	82.6 % (71 of 86)	82.6 % (71 of 86)
Aromatic	70.0 % (21 of 30)	70.0 % (21 of 30)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')

GGAGGAGGAG GA

2. P16

GQWNKPSKPK TN

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
2	P16	natural abundance	protein	1 mM
3	potassium phosphate	natural abundance		10 mM
4	potassium chloride	natural abundance		10 mM
5	DSS	natural abundance		0.01 mM
6	sodium azide	natural abundance		3 mM
7	H2O		solvent	95 %
8	D2O		solvent	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
9	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
10	P16	natural abundance	protein	1 mM
11	potassium phosphate	natural abundance		10 mM
12	potassium chloride	natural abundance		10 mM
13	DSS	natural abundance		0.01 mM
14	sodium azide	natural abundance		3 mM
15	D2O		solvent	100 %

Protein Blocks Logo

Calculated from 5 models in PDB: 2RU7, Strand ID: C, D Detail

Release date

2013-02-10

Citation

Anti-prion activity of an RNA aptamer and its structural basis
Mashima, T., Nishikawa, F., Kamatari, Y.O., Fujiwara, H., Saimura, M., Nagata, T., Kodaki, T., Nishikawa, S., Kuwata, K., Katahira, M.
Nucleic Acids Res. (2013), 41, 1355-1362, PubMed 23180780 , DOI 10.1093/nar/gks1132 , Abstract

Related entities 1. RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3'), : 1 : 14 : 6 entities Detail

Related entities 2. P16, : 1 : 11 : 54 : 5 entities Detail

Interaction partners 2. P16, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
2	P16	natural abundance	protein	1 mM
3	potassium phosphate	natural abundance		10 mM
4	potassium chloride	natural abundance		10 mM
5	DSS	natural abundance		0.01 mM
6	sodium azide	natural abundance		3 mM
7	H2O		solvent	95 %
8	D2O		solvent	5 %

2 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
2	P16	natural abundance	protein	1 mM
3	potassium phosphate	natural abundance		10 mM
4	potassium chloride	natural abundance		10 mM
5	DSS	natural abundance		0.01 mM
6	sodium azide	natural abundance		3 mM
7	H2O		solvent	95 %
8	D2O		solvent	5 %

3 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
9	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
10	P16	natural abundance	protein	1 mM
11	potassium phosphate	natural abundance		10 mM
12	potassium chloride	natural abundance		10 mM
13	DSS	natural abundance		0.01 mM
14	sodium azide	natural abundance		3 mM
15	D2O		solvent	100 %

4 2D 1H-1H NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
9	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
10	P16	natural abundance	protein	1 mM
11	potassium phosphate	natural abundance		10 mM
12	potassium chloride	natural abundance		10 mM
13	DSS	natural abundance		0.01 mM
14	sodium azide	natural abundance		3 mM
15	D2O		solvent	100 %

5 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
2	P16	natural abundance	protein	1 mM
3	potassium phosphate	natural abundance		10 mM
4	potassium chloride	natural abundance		10 mM
5	DSS	natural abundance		0.01 mM
6	sodium azide	natural abundance		3 mM
7	H2O		solvent	95 %
8	D2O		solvent	5 %

6 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
9	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
10	P16	natural abundance	protein	1 mM
11	potassium phosphate	natural abundance		10 mM
12	potassium chloride	natural abundance		10 mM
13	DSS	natural abundance		0.01 mM
14	sodium azide	natural abundance		3 mM
15	D2O		solvent	100 %

7 2D DQF-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
2	P16	natural abundance	protein	1 mM
3	potassium phosphate	natural abundance		10 mM
4	potassium chloride	natural abundance		10 mM
5	DSS	natural abundance		0.01 mM
6	sodium azide	natural abundance		3 mM
7	H2O		solvent	95 %
8	D2O		solvent	5 %

8 2D DQF-COSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
9	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
10	P16	natural abundance	protein	1 mM
11	potassium phosphate	natural abundance		10 mM
12	potassium chloride	natural abundance		10 mM
13	DSS	natural abundance		0.01 mM
14	sodium azide	natural abundance		3 mM
15	D2O		solvent	100 %

9 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
9	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
10	P16	natural abundance	protein	1 mM
11	potassium phosphate	natural abundance		10 mM
12	potassium chloride	natural abundance		10 mM
13	DSS	natural abundance		0.01 mM
14	sodium azide	natural abundance		3 mM
15	D2O		solvent	100 %

10 JRHMBC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.2

#	Name	Isotope labeling	Type	Concentration
1	RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3')	natural abundance	RNA	1 mM
2	P16	natural abundance	protein	1 mM
3	potassium phosphate	natural abundance		10 mM
4	potassium chloride	natural abundance		10 mM
5	DSS	natural abundance		0.01 mM
6	sodium azide	natural abundance		3 mM
7	H2O		solvent	95 %
8	D2O		solvent	5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_11489_2ru7.nef
Input source #2: Coordindates	2ru7.cif
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

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--
GGAGGAGGAGGA
||||||||||||
GGAGGAGGAGGA

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------20----
GGAGGAGGAGGA
||||||||||||
GGAGGAGGAGGA
--------10--

Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C

----30------
GQWNKPSKPKTN
||||||||||||
GQWNKPSKPKTN
--------10--

Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D

--40--------
GQWNKPSKPKTN
||||||||||||
GQWNKPSKPKTN
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	12	100.0
B	B	12	100.0
C	C	12	100.0
D	D	12	100.0

Content subtype: combined_11489_2ru7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	153		100.0 (chain: A, length: 12), 100.0 (chain: C, length: 12)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3152 (1)	noe	100.0 (chain: A, length: 12), 100.0 (chain: B, length: 12), 100.0 (chain: C, length: 12), 100.0 (chain: D, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 153
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: C
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	85	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	69	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	16	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	16	16	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	68	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	13	56.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	55	88.7

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	5	83.3

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 12, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 12, Sequence coverage: 100.0%
- Total number of restraints: 3144
- Weight of restraints: 1.0 (3144)
- Potential type of restraints: upper-bound-parabolic (3144)
- Range of distance target values: 1.8, 1.8 (Å)
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map

Keywords Alzheimer's disease, Aptamer, NMR, Prion, RNA

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Found 1 Document (0.733 seconds)

BMRB: 11489

Sample #1

Sample #2

Related entities 1. RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'), : 1 : 14 : 6 entities Detail

Related entities 2. P16, : 1 : 11 : 54 : 5 entities Detail

Interaction partners 2. P16, : 1 interactors Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail

Related entities 1. RNA (5'-R(GPGPAPGPGPAPGPGPAPGPGPA)-3'), : 1 : 14 : 6 entities Detail