BMRBj - BMREntryMaster

Found 1 Document (0.673 seconds)

BMRB: 11014

2RN1

Liquid crystal solution structure of the kissing complex formed by the apical loop of the HIV TAR RNA and a high affinity RNA aptamer optimized by SELEX.

Authors

Van Melckebeke, H., Devany, M., Di Primo, C., Beaurain, F., Toulme, J., Bryce, D.L., Boisbouvier, J.

Assembly

TAR-TAR*GA aptamer kissing complex

Entity

1. TAR (polymer, Thiol state: not present), 16 monomers, 5231.107 Da Detail

GAGCCCUGGG AGGCUC

2. TAR*GA (polymer, Thiol state: not present), 16 monomers, 5175.083 Da Detail

GCUGGUCCCA GACAGC

Total weight

10406.189 Da

Max. entity weight

5231.107 Da

Source organism

Human immunodeficiency virus 1

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 80.4 %, Completeness (bb): 87.8 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	80.4 % (410 of 510)	83.3 % (235 of 282)	82.5 % (175 of 212)	0.0 % (0 of 16)
Suger, PO4	87.8 % (309 of 352)	87.0 % (167 of 192)	88.7 % (142 of 160)
Nucleobase	63.9 % (101 of 158)	75.6 % (68 of 90)	63.5 % (33 of 52)	0.0 % (0 of 16)
Aromatic	74.3 % (101 of 136)	100.0 % (68 of 68)	63.5 % (33 of 52)	0.0 % (0 of 16)

1. TAR

GAGCCCUGGG AGGCUC

2. TAR*GA

GCUGGUCCCA GACAGC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
37	TAR	natural abundance	1.8 mM
38	TAR*GA	[U-98% 13C; U-98% 15N]	0.9 mM
39	sodium phosphate	natural abundance	10 mM
40	sodium chloride	natural abundance	50 mM
41	EDTA	natural abundance	10 uM
42	sodium azide	natural abundance	0.4 g/L

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
43	TAR	[U-98% 13C; U-98% 15N]	0.9 mM
44	TAR*GA	natural abundance	1.8 mM
45	sodium phosphate	natural abundance	10 mM
46	sodium chloride	natural abundance	50 mM
47	EDTA	natural abundance	10 uM
48	sodium azide	natural abundance	0.4 g/L

Release date

2008-07-14

Citation

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex
Van Melckebeke, H., Devany, M., Di Primo, C., Beaurain, F., Toulme, J., Bryce, D.L., Boisbouvier, J.
Proc. Natl. Acad. Sci. U. S. A. (2008), 105, 9210-9215, PubMed 18607001 , DOI 10.1073/pnas.0712121105 , Abstract

Related entities 1. TAR, : 1 : 1 : 30 entities Detail

Related entities 2. TAR*GA, : 1 : 1 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.6

#	Name	Isotope labeling	Concentration
7	TAR	natural abundance	1.1 mM
8	TAR*GA	natural abundance	1.1 mM
9	sodium phosphate	natural abundance	10 mM
10	sodium chloride	natural abundance	50 mM
11	EDTA	natural abundance	10 uM
12	sodium azide	natural abundance	0.4 g/L

2 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	TAR	natural abundance	1.3 mM
2	TAR*GA	natural abundance	1.3 mM
3	sodium phosphate	natural abundance	10 mM
4	sodium chloride	natural abundance	50 mM
5	EDTA	natural abundance	10 uM
6	sodium azide	natural abundance	0.4 g/L

3 3D 1H-13C TROSY NOESY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
37	TAR	natural abundance	1.8 mM
38	TAR*GA	[U-98% 13C; U-98% 15N]	0.9 mM
39	sodium phosphate	natural abundance	10 mM
40	sodium chloride	natural abundance	50 mM
41	EDTA	natural abundance	10 uM
42	sodium azide	natural abundance	0.4 g/L

4 2D JNN-COSY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.6

#	Name	Isotope labeling	Concentration
13	TAR	[U-98% 13C; U-98% 15N]	0.37 mM
14	TAR*GA	natural abundance	0.74 mM
15	sodium phosphate	natural abundance	10 mM
16	sodium chloride	natural abundance	50 mM
17	EDTA	natural abundance	10 uM
18	sodium azide	natural abundance	0.4 g/L

5 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
37	TAR	natural abundance	1.8 mM
38	TAR*GA	[U-98% 13C; U-98% 15N]	0.9 mM
39	sodium phosphate	natural abundance	10 mM
40	sodium chloride	natural abundance	50 mM
41	EDTA	natural abundance	10 uM
42	sodium azide	natural abundance	0.4 g/L

6 3D HCCH-COSY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
43	TAR	[U-98% 13C; U-98% 15N]	0.9 mM
44	TAR*GA	natural abundance	1.8 mM
45	sodium phosphate	natural abundance	10 mM
46	sodium chloride	natural abundance	50 mM
47	EDTA	natural abundance	10 uM
48	sodium azide	natural abundance	0.4 g/L

7 3D HCN

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
37	TAR	natural abundance	1.8 mM
38	TAR*GA	[U-98% 13C; U-98% 15N]	0.9 mM
39	sodium phosphate	natural abundance	10 mM
40	sodium chloride	natural abundance	50 mM
41	EDTA	natural abundance	10 uM
42	sodium azide	natural abundance	0.4 g/L

8 3D HCN

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
43	TAR	[U-98% 13C; U-98% 15N]	0.9 mM
44	TAR*GA	natural abundance	1.8 mM
45	sodium phosphate	natural abundance	10 mM
46	sodium chloride	natural abundance	50 mM
47	EDTA	natural abundance	10 uM
48	sodium azide	natural abundance	0.4 g/L

9 2D intra base TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
37	TAR	natural abundance	1.8 mM
38	TAR*GA	[U-98% 13C; U-98% 15N]	0.9 mM
39	sodium phosphate	natural abundance	10 mM
40	sodium chloride	natural abundance	50 mM
41	EDTA	natural abundance	10 uM
42	sodium azide	natural abundance	0.4 g/L

10 3D 1H-13C TROSY NOESY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
43	TAR	[U-98% 13C; U-98% 15N]	0.9 mM
44	TAR*GA	natural abundance	1.8 mM
45	sodium phosphate	natural abundance	10 mM
46	sodium chloride	natural abundance	50 mM
47	EDTA	natural abundance	10 uM
48	sodium azide	natural abundance	0.4 g/L

11 2D intra base TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
43	TAR	[U-98% 13C; U-98% 15N]	0.9 mM
44	TAR*GA	natural abundance	1.8 mM
45	sodium phosphate	natural abundance	10 mM
46	sodium chloride	natural abundance	50 mM
47	EDTA	natural abundance	10 uM
48	sodium azide	natural abundance	0.4 g/L

12 13C-1H spin state selective experiments

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
43	TAR	[U-98% 13C; U-98% 15N]	0.9 mM
44	TAR*GA	natural abundance	1.8 mM
45	sodium phosphate	natural abundance	10 mM
46	sodium chloride	natural abundance	50 mM
47	EDTA	natural abundance	10 uM
48	sodium azide	natural abundance	0.4 g/L

13 13C-1H spin state selective experiments

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Concentration
37	TAR	natural abundance	1.8 mM
38	TAR*GA	[U-98% 13C; U-98% 15N]	0.9 mM
39	sodium phosphate	natural abundance	10 mM
40	sodium chloride	natural abundance	50 mM
41	EDTA	natural abundance	10 uM
42	sodium azide	natural abundance	0.4 g/L

14 2D JNN-COSY

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.6

#	Name	Isotope labeling	Concentration
19	TAR	natural abundance	0.74 mM
20	TAR*GA	[U-98% 13C; U-98% 15N]	0.37 mM
21	sodium phosphate	natural abundance	10 mM
22	sodium chloride	natural abundance	50 mM
23	EDTA	natural abundance	10 uM
24	sodium azide	natural abundance	0.4 g/L

15 13C-1H spin state selective experiments

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Solution containing Pf1 filamentous phages (D2O splitting =12.4 Hz).

#	Name	Isotope labeling	Concentration
25	TAR	natural abundance	1.6 mM
26	TAR*GA	[U-98% 13C; U-98% 15N]	0.8 mM
27	sodium phosphate	natural abundance	10 mM
28	sodium chloride	natural abundance	50 mM
29	EDTA	natural abundance	10 uM
30	sodium azide	natural abundance	0.4 g/L

16 13C-1H spin state selective experiments

Instrument

Varian INOVA - 800 MHz equipped with a cryogenic probe

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6, Details Solution containing Pf1 filamentous phages (D2O splitting =14.0 Hz).

#	Name	Isotope labeling	Concentration
31	TAR	[U-98% 13C; U-98% 15N]	0.5 mM
32	TAR*GA	natural abundance	1.0 mM
33	sodium phosphate	natural abundance	10 mM
34	sodium chloride	natural abundance	50 mM
35	EDTA	natural abundance	10 uM
36	sodium azide	natural abundance	0.4 g/L

nullKeywords high stability RNA aptamer selected by SELEX, HIV TAR RNA, Kissing complex, liquid crystal NMR, GA base pair, High affinity RNA aptamer selected by SELEX, HIV TAR, Liquid crystal NMR, RNA kissing complex

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.673 seconds)

BMRB: 11014

Sample #1

Sample #2

Related entities 1. TAR, : 1 : 1 : 30 entities Detail

Related entities 2. TAR*GA, : 1 : 1 entities Detail

Experiments performed 16 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample