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BMRB: 25661

5LWJ

1H, 13C, and 15N chemical shift assignments of a the GTP class II RNA aptamer in complex with GTP

Authors

Wolter, A.C., Duchardt-Ferner, E., Nasiri, A., Wunderlich, C.H., Kreutz, C., Woehnert, J.

Assembly

rna-ligand complex

Entity

1. GTP class II aptamer (polymer, Thiol state: not present), 34 monomers, 11079.64 Da Detail

GGCAGCCAGA XGAGCACGUA UACGCAAGGC UGUC

2. N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE (non-polymer), 348.229 Da
3. GUANOSINE-5'-TRIPHOSPHATE (non-polymer), 523.180 Da
4. MAGNESIUM ION (non-polymer), 24.305 Da

Total weight

11975.354 Da

Max. entity weight

11079.64 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 97.1 %, Completeness: 93.3 %, Completeness (bb): 92.2 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	93.3 % (517 of 554)	97.6 % (279 of 286)	100.0 % (220 of 220)	80.0 % (12 of 15)	18.2 % (6 of 33)
Suger, PO4	92.2 % (365 of 396)	98.0 % (194 of 198)	100.0 % (165 of 165)		18.2 % (6 of 33)
Nucleobase	96.2 % (152 of 158)	96.6 % (85 of 88)	100.0 % (55 of 55)	80.0 % (12 of 15)
Aromatic	95.7 % (134 of 140)	95.7 % (67 of 70)	100.0 % (55 of 55)	80.0 % (12 of 15)

1. GTP class II aptamer

GGCAGCCAGA XGAGCACGUA UACGCAAGGC UGUC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II unlabeled

#	Name	Isotope labeling	Concentration
1	GTP class II aptamer	natural abundance	0.66 mM
2	GTP	[U-13C; U-15N]	1.32 mM
3	magnesium acetate	natural abundance	2 mM
4	potassium chloride	natural abundance	25 mM
5	potassium phosphate	natural abundance	25 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II unlabeled

#	Name	Isotope labeling	Concentration
8	GTP class II aptamer	natural abundance	0.66 mM
9	GTP	[U-13C; U-15N]	1.32 mM
10	magnesium acetate	natural abundance	2 mM
11	potassium chloride	natural abundance	25 mM
12	potassium phosphate	natural abundance	25 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II unlabeled

#	Name	Isotope labeling	Concentration
14	GTP class II aptamer	natural abundance	0.9 mM
15	GTP	[U-13C; U-15N]	1.8 mM
16	magnesium acetate	natural abundance	2 mM
17	potassium chloride	natural abundance	25 mM
18	potassium phosphate	natural abundance	25 mM
19	H2O	natural abundance	95 %
20	D2O	natural abundance	5 %

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 15N uniformly labeled

#	Name	Isotope labeling	Concentration
21	GTP class II aptamer	[U-15N]	0.33 mM
22	GTP	[U-13C; U-15N]	0.5 mM
23	magnesium acetate	natural abundance	2 mM
24	potassium chloride	natural abundance	25 mM
25	potassium phosphate	natural abundance	25 mM
26	H2O	natural abundance	95 %
27	D2O	natural abundance	5 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N uniformly labeled

#	Name	Isotope labeling	Concentration
28	GTP class II aptamer	[U-13C; U-15N]	0.36 mM
29	GTP	natural abundance	0.72 mM
30	magnesium acetate	natural abundance	2 mM
31	potassium chloride	natural abundance	25 mM
32	potassium phosphate	natural abundance	25 mM
33	H2O	natural abundance	90 %
34	D2O	natural abundance	10 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N uniformly labeled

#	Name	Isotope labeling	Concentration
35	GTP class II aptamer	[U-13C; U-15N]	1.2 mM
36	GTP	natural abundance	2.4 mM
37	magnesium acetate	natural abundance	2 mM
38	potassium chloride	natural abundance	25 mM
39	potassium phosphate	natural abundance	25 mM
40	D2O	natural abundance	100 %

Sample #7

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Ade labeled

#	Name	Isotope labeling	Concentration
41	GTP class II aptamer	[U-13C; U-15N]-Ade	1.1 mM
42	GTP	[U-13C; U-15N]	2.2 mM
43	magnesium acetate	natural abundance	2 mM
44	potassium chloride	natural abundance	25 mM
45	potassium phosphate	natural abundance	25 mM
46	H2O	natural abundance	95 %
47	D2O	natural abundance	5 %

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Ade labeled

#	Name	Isotope labeling	Concentration
48	GTP class II aptamer	[U-13C; U-15N]-Ade	1.1 mM
49	GTP	[U-13C; U-15N]	2.2 mM
50	magnesium acetate	natural abundance	2 mM
51	potassium chloride	natural abundance	25 mM
52	potassium phosphate	natural abundance	25 mM
53	D2O	natural abundance	100 %

Sample #9

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Cyt labeled

#	Name	Isotope labeling	Concentration
54	GTP class II aptamer	[U-13C; U-15N]-Cyt	0.73 mM
55	GTP	[U-15N]	1.46 mM
56	magnesium acetate	natural abundance	2 mM
57	potassium chloride	natural abundance	25 mM
58	potassium phosphate	natural abundance	25 mM
59	H2O	natural abundance	95 %
60	D2O	natural abundance	5 %

Sample #10

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Cyt labeled

#	Name	Isotope labeling	Concentration
61	GTP class II aptamer	[U-13C; U-15N]-Cyt	0.73 mM
62	GTP	[U-15N]	1.46 mM
63	magnesium acetate	natural abundance	2 mM
64	potassium chloride	natural abundance	25 mM
65	potassium phosphate	natural abundance	25 mM
66	D2O	natural abundance	100 %

Sample #11

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-GuaUri labeled

#	Name	Isotope labeling	Concentration
67	GTP class II aptamer	[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura	0.82 mM
68	GTP	natural abundance	1.64 mM
69	magnesium acetate	natural abundance	2 mM
70	potassium chloride	natural abundance	25 mM
71	potassium phosphate	natural abundance	25 mM
72	H2O	natural abundance	95 %
73	D2O	natural abundance	5 %

Sample #12

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-GuaUri labeled

#	Name	Isotope labeling	Concentration
74	GTP class II aptamer	[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura	0.82 mM
75	GTP	[U-15N]	1.64 mM
76	magnesium acetate	natural abundance	2 mM
77	potassium chloride	natural abundance	25 mM
78	potassium phosphate	natural abundance	25 mM
79	D2O	natural abundance	100 %

Chem. Shift Complete2

Sequence coverage: 0.0 %, Completeness: 46.7 %, Completeness (bb): 46.1 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	46.7 % (517 of 1108)	48.8 % (279 of 572)	50.0 % (220 of 440)	40.0 % (12 of 30)	9.1 % (6 of 66)
Suger, PO4	46.1 % (365 of 792)	49.0 % (194 of 396)	50.0 % (165 of 330)		9.1 % (6 of 66)
Nucleobase	48.1 % (152 of 316)	48.3 % (85 of 176)	50.0 % (55 of 110)	40.0 % (12 of 30)
Aromatic	47.9 % (134 of 280)	47.9 % (67 of 140)	50.0 % (55 of 110)	40.0 % (12 of 30)

1. GTP class II aptamer

GGCAGCCAGA XGAGCACGUA UACGCAAGGC UGUC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II unlabeled

#	Name	Isotope labeling	Concentration
1	GTP class II aptamer	natural abundance	0.66 mM
2	GTP	[U-13C; U-15N]	1.32 mM
3	magnesium acetate	natural abundance	2 mM
4	potassium chloride	natural abundance	25 mM
5	potassium phosphate	natural abundance	25 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II unlabeled

#	Name	Isotope labeling	Concentration
8	GTP class II aptamer	natural abundance	0.66 mM
9	GTP	[U-13C; U-15N]	1.32 mM
10	magnesium acetate	natural abundance	2 mM
11	potassium chloride	natural abundance	25 mM
12	potassium phosphate	natural abundance	25 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II unlabeled

#	Name	Isotope labeling	Concentration
14	GTP class II aptamer	natural abundance	0.9 mM
15	GTP	[U-13C; U-15N]	1.8 mM
16	magnesium acetate	natural abundance	2 mM
17	potassium chloride	natural abundance	25 mM
18	potassium phosphate	natural abundance	25 mM
19	H2O	natural abundance	95 %
20	D2O	natural abundance	5 %

Sample #4

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 15N uniformly labeled

#	Name	Isotope labeling	Concentration
21	GTP class II aptamer	[U-15N]	0.33 mM
22	GTP	[U-13C; U-15N]	0.5 mM
23	magnesium acetate	natural abundance	2 mM
24	potassium chloride	natural abundance	25 mM
25	potassium phosphate	natural abundance	25 mM
26	H2O	natural abundance	95 %
27	D2O	natural abundance	5 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N uniformly labeled

#	Name	Isotope labeling	Concentration
28	GTP class II aptamer	[U-13C; U-15N]	0.36 mM
29	GTP	natural abundance	0.72 mM
30	magnesium acetate	natural abundance	2 mM
31	potassium chloride	natural abundance	25 mM
32	potassium phosphate	natural abundance	25 mM
33	H2O	natural abundance	90 %
34	D2O	natural abundance	10 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N uniformly labeled

#	Name	Isotope labeling	Concentration
35	GTP class II aptamer	[U-13C; U-15N]	1.2 mM
36	GTP	natural abundance	2.4 mM
37	magnesium acetate	natural abundance	2 mM
38	potassium chloride	natural abundance	25 mM
39	potassium phosphate	natural abundance	25 mM
40	D2O	natural abundance	100 %

Sample #7

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Ade labeled

#	Name	Isotope labeling	Concentration
41	GTP class II aptamer	[U-13C; U-15N]-Ade	1.1 mM
42	GTP	[U-13C; U-15N]	2.2 mM
43	magnesium acetate	natural abundance	2 mM
44	potassium chloride	natural abundance	25 mM
45	potassium phosphate	natural abundance	25 mM
46	H2O	natural abundance	95 %
47	D2O	natural abundance	5 %

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Ade labeled

#	Name	Isotope labeling	Concentration
48	GTP class II aptamer	[U-13C; U-15N]-Ade	1.1 mM
49	GTP	[U-13C; U-15N]	2.2 mM
50	magnesium acetate	natural abundance	2 mM
51	potassium chloride	natural abundance	25 mM
52	potassium phosphate	natural abundance	25 mM
53	D2O	natural abundance	100 %

Sample #9

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Cyt labeled

#	Name	Isotope labeling	Concentration
54	GTP class II aptamer	[U-13C; U-15N]-Cyt	0.73 mM
55	GTP	[U-15N]	1.46 mM
56	magnesium acetate	natural abundance	2 mM
57	potassium chloride	natural abundance	25 mM
58	potassium phosphate	natural abundance	25 mM
59	H2O	natural abundance	95 %
60	D2O	natural abundance	5 %

Sample #10

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-Cyt labeled

#	Name	Isotope labeling	Concentration
61	GTP class II aptamer	[U-13C; U-15N]-Cyt	0.73 mM
62	GTP	[U-15N]	1.46 mM
63	magnesium acetate	natural abundance	2 mM
64	potassium chloride	natural abundance	25 mM
65	potassium phosphate	natural abundance	25 mM
66	D2O	natural abundance	100 %

Sample #11

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-GuaUri labeled

#	Name	Isotope labeling	Concentration
67	GTP class II aptamer	[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura	0.82 mM
68	GTP	natural abundance	1.64 mM
69	magnesium acetate	natural abundance	2 mM
70	potassium chloride	natural abundance	25 mM
71	potassium phosphate	natural abundance	25 mM
72	H2O	natural abundance	95 %
73	D2O	natural abundance	5 %

Sample #12

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.3, Details GTP Cl II 13C15N-GuaUri labeled

#	Name	Isotope labeling	Concentration
74	GTP class II aptamer	[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura	0.82 mM
75	GTP	[U-15N]	1.64 mM
76	magnesium acetate	natural abundance	2 mM
77	potassium chloride	natural abundance	25 mM
78	potassium phosphate	natural abundance	25 mM
79	D2O	natural abundance	100 %

Release date

2016-09-14

Citation 1

NMR resonance assignments for the class II GTP binding RNA aptamer in complex with GTP
Wolter, A.C., Duchardt-Ferner, E., Nasiri, A., Hantke, K., Wunderlich, C.H., Kreutz, C., Woehnert, J.
Biomol. NMR Assign. (2016), 10, 101-105, PubMed 26373429 , DOI 10.1007/s12104-015-9646-7 , Abstract

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Citation 2

Informational complexity and functional activity of RNA structures
Carothers, J.M., Oestreich, S.C., Davis, J.H., Szostak, J.W.
J. Am. Chem. Soc. (2004), 126, 5130-5137, PubMed 15099096 , DOI 10.1021/ja031504a , Abstract

Citation 3

Aptamers selected for higher-affinity binding are not more specific for the target ligand
Carothers, J.M., Oestreich, S.C., Szostak, J.W.
J. Am. Chem. Soc. (2006), 128, 7929-7937, PubMed 16771507 , DOI 10.1021/ja060952q , Abstract

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