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BMRB: 7090

2GVO

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides

Authors

Joli, F., Bouchemal, N., Laigle, A., Hartmann, B., Hantz, E.

Assembly

18 mer hairpin hexaloop

Entity

1. 18 mer hairpin hexaloop (polymer, Thiol state: not present), 18 monomers, 5907.486 Da Detail

GAGGUCGGGA UGGAUCUC

Formula weight

5907.486 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 87.1 %, Completeness (bb): 99.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	87.1 % (263 of 302)	96.8 % (149 of 154)	76.3 % (90 of 118)	58.3 % (7 of 12)	94.4 % (17 of 18)
Suger, PO4	99.5 % (215 of 216)	100.0 % (108 of 108)	100.0 % (90 of 90)		94.4 % (17 of 18)
Nucleobase	55.8 % (48 of 86)	89.1 % (41 of 46)	0.0 % (0 of 28)	58.3 % (7 of 12)
Aromatic	52.5 % (42 of 80)	87.5 % (35 of 40)	0.0 % (0 of 28)	58.3 % (7 of 12)

1. 18mer hairpin hexaloop

GAGGUCGGGA UGGAUCUC

Show sample condition

Sample

pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

Release date

2007-04-26

Citation

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides
Joli, F., Bouchemal, N., Laigle, A., Hartmann, B., Hantz, E.
Nucleic Acids Res. (2006), 34, 5740-5751, PubMed 17041234 , DOI 10.1093/nar/gkl617 , Abstract

Related entities 1. 18 mer hairpin hexaloop, : 1 entities Detail

Experiments performed 9 experiments Detail

1 1H15N HSQC

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

2 1H13C HSQC

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

3 1H1H13C HCCH COSY

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

4 1H1H13C NOESY HSQC

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

5 HNN COSY

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

6 1H1H13C HSCQ TOCSY

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

7 HCN TROSY

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

8 CU HNCCCH

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

9 GA HNC TOCSY CH

Instrument

Varian UnityInova - 500 MHz Two probes: 5mm gradient indirect detection, 5mm triple (1H, 13C, 15N) detection.

Sample

State isotropic, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	18mer hairpin hexaloop	[U-98% 13C; U-98% 15N]	RNA	1 mM
2	phosphate buffer		buffer	10 mM
3	EDTA		chelating agent	0.01 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr7090_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: bmr7090_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	277		100.0 (chain: 1, length: 18)
1	Chemical shift references	chemical_shift_referencing	OK	4		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: 1, Chain length: 18, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 149
- ¹⁵N chemical shifts: 21
- ¹³C chemical shifts: 90
- ³¹P chemical shifts: 17

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	N9	168.1
1	G	P	-0.19
2	A	N9	167.78
2	A	P	-0.45
3	G	N9	169.0
3	G	P	-0.45
4	G	P	-0.83
5	U	N1	163.22
5	U	P	-0.03
6	C	N4	97.51
6	C	P	-0.16
7	G	N9	167.73
7	G	P	-0.9
8	G	P	-0.0
9	G	N9	168.39
9	G	P	0.3
10	A	N9	167.11
10	A	P	-0.03
11	U	P	0.03
12	G	N9	168.38
12	G	P	0.17
13	G	P	-0.77
14	A	N9	167.75
14	A	P	-0.19
15	U	N1	159.32
15	U	P	-0.54
16	C	N4	97.55
16	C	P	-0.54
17	U	N1	159.63
17	U	P	-0.02
18	C	N4	97.51

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	149	96.8
¹⁵N chemical shifts	12	7	58.3
¹³C chemical shifts	118	90	76.3

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	108	100.0
¹³C chemical shifts	90	90	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	41	89.1
¹⁵N chemical shifts	12	7	58.3
¹³C chemical shifts	28	0	0.0

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	14	14	100.0
¹³C chemical shifts	14	0	0.0

Histogram of normalized assigned chemical shifts

Keywords 13C/15N-labeled RNA, G.U wobble pair, hairpin structure, hexaloop, RNA structure