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BMRB: 19662

2MI0

NMR structure of the I-V kissing-loop interaction of the Neurospora VS ribozyme

Authors

Bouchard, P., Legault, P.

Assembly

I-V kissing-loop interaction of the Neurospora VS ribozyme

Entity

1. RNA (5'-R(*GP*AP*GP*CP*AP*GP*CP*AP*UP*CP*GP*UP*CP*GP*GP*CP*UP*GP*CP*UP*CP*A)-3') (polymer, Thiol state: not present), 22 monomers, 7112.213 Da Detail

GAGCAGCAUC GUCGGCUGCU CA

2. RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3') (polymer, Thiol state: not present), 21 monomers, 6783.991 Da Detail

GCGGCAGUUG ACUACUGUCG C

Total weight

13896.204 Da

Max. entity weight

7112.213 Da

Source organism

Neurospora crassa

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 62.8 %, Completeness (bb): 49.3 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	62.8 % (433 of 689)	60.9 % (231 of 379)	64.8 % (186 of 287)	69.6 % (16 of 23)
Suger, PO4	49.3 % (233 of 473)	45.7 % (118 of 258)	53.5 % (115 of 215)
Nucleobase	92.6 % (200 of 216)	93.4 % (113 of 121)	98.6 % (71 of 72)	69.6 % (16 of 23)
Aromatic	92.1 % (175 of 190)	92.6 % (88 of 95)	98.6 % (71 of 72)	69.6 % (16 of 23)

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

GAGCAGCAUC GUCGGCUGCU CA

2. RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3')

GCGGCAGUUG ACUACUGUCG C

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.5 mM
8	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-13C; U-15N]	1.5 mM
9	TRIS	[U-2H]	10 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.05 mM
12	magnesium chloride	natural abundance	5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
19	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]	1.7 mM
20	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.7 mM
21	TRIS	[U-2H]	10 mM
22	sodium chloride	natural abundance	50 mM
23	sodium azide	natural abundance	0.05 mM
24	magnesium chloride	natural abundance	5 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
25	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
26	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
27	TRIS	[U-2H]	10 mM
28	sodium chloride	natural abundance	50 mM
29	sodium azide	natural abundance	0.05 mM
30	magnesium chloride	natural abundance	5 mM

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details The labeling is actually [U-13C;U-15N]-Gua+Cyt, but is not in the choice

#	Name	Isotope labeling	Concentration
31	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
32	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
33	TRIS	[U-2H]	10 mM
34	sodium chloride	natural abundance	50 mM
35	sodium azide	natural abundance	0.05 mM
36	magnesium chloride	natural abundance	5 mM

Sample #7

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
37	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
38	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
39	TRIS	[U-2H]	10 mM
40	sodium chloride	natural abundance	50 mM
41	sodium azide	natural abundance	0.05 mM
42	magnesium chloride	natural abundance	5 mM

Sample #8

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
43	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 mM
44	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 mM
45	TRIS	[U-2H]	10 mM
46	sodium chloride	natural abundance	50 mM
47	sodium azide	natural abundance	0.05 mM
48	magnesium chloride	natural abundance	5 mM

Sample #9

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
49	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]	1.7 mM
50	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.7 mM
51	TRIS	[U-2H]	10 mM
52	sodium chloride	natural abundance	50 mM
53	sodium azide	natural abundance	0.05 mM
54	magnesium chloride	natural abundance	5 mM

Sample #10

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
55	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.5 mM
56	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-13C; U-15N]	1.5 mM
57	TRIS	[U-2H]	10 mM
58	sodium chloride	natural abundance	50 mM
59	sodium azide	natural abundance	0.05 mM
60	magnesium chloride	natural abundance	5 mM

Sample #11

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
61	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	0.2 ~ 0.3 mM
62	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	0.2 ~ 0.3 mM
63	TRIS	[U-2H]	10 mM
64	sodium chloride	natural abundance	50 mM
65	sodium azide	natural abundance	0.05 mM
66	magnesium chloride	natural abundance	5 mM
67	Pf1 phage	natural abundance	14.6-20.5 mg/mL

Release date

2014-01-09

Citation

Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction
Bouchard, P., Legault, P.
Biochemistry (2014), 53, 258-269, PubMed 24325625 , DOI 10.1021/bi401491g , Abstract

Related entities 1. RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3'), : 1 entities Detail

Related entities 2. RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3'), : 1 entities Detail

Experiments performed 33 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

3 2D 1H-15N HSQC NH2 only

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

4 2D 1H-15N HSQC NH2 only

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

5 2D 1H-15N NHH COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

6 2D 1H-15N NHH COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

7 2D 1H-15N HMQC J=21Hz

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
37	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
38	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
39	TRIS	[U-2H]	10 mM
40	sodium chloride	natural abundance	50 mM
41	sodium azide	natural abundance	0.05 mM
42	magnesium chloride	natural abundance	5 mM

8 2D 1H-15N HMQC J=21Hz

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
43	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 mM
44	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 mM
45	TRIS	[U-2H]	10 mM
46	sodium chloride	natural abundance	50 mM
47	sodium azide	natural abundance	0.05 mM
48	magnesium chloride	natural abundance	5 mM

9 2D 1H-15N CPMG NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

10 2D 1H-15N CPMG NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

11 2D 1H-1H flip-back watergate NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

12 3D 15N-edited NOESY-HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

13 3D 15N-edited NOESY-HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

14 2D 1H-13C CT-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.5 mM
8	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-13C; U-15N]	1.5 mM
9	TRIS	[U-2H]	10 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.05 mM
12	magnesium chloride	natural abundance	5 mM

15 2D 1H-13C CT-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
19	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]	1.7 mM
20	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.7 mM
21	TRIS	[U-2H]	10 mM
22	sodium chloride	natural abundance	50 mM
23	sodium azide	natural abundance	0.05 mM
24	magnesium chloride	natural abundance	5 mM

16 2D 1H-13C CT-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
25	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
26	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
27	TRIS	[U-2H]	10 mM
28	sodium chloride	natural abundance	50 mM
29	sodium azide	natural abundance	0.05 mM
30	magnesium chloride	natural abundance	5 mM

17 2D 1H-13C CT-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details The labeling is actually [U-13C;U-15N]-Gua+Cyt, but is not in the choice

#	Name	Isotope labeling	Concentration
31	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
32	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
33	TRIS	[U-2H]	10 mM
34	sodium chloride	natural abundance	50 mM
35	sodium azide	natural abundance	0.05 mM
36	magnesium chloride	natural abundance	5 mM

18 3D 15N/13C-edited NOESY-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
49	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]	1.7 mM
50	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.7 mM
51	TRIS	[U-2H]	10 mM
52	sodium chloride	natural abundance	50 mM
53	sodium azide	natural abundance	0.05 mM
54	magnesium chloride	natural abundance	5 mM

19 3D 15N/13C-edited NOESY-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
55	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.5 mM
56	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-13C; U-15N]	1.5 mM
57	TRIS	[U-2H]	10 mM
58	sodium chloride	natural abundance	50 mM
59	sodium azide	natural abundance	0.05 mM
60	magnesium chloride	natural abundance	5 mM

20 3D 13C-edited HMQC-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.5 mM
8	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-13C; U-15N]	1.5 mM
9	TRIS	[U-2H]	10 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.05 mM
12	magnesium chloride	natural abundance	5 mM

21 3D 13C-edited HMQC-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
19	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]	1.7 mM
20	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.7 mM
21	TRIS	[U-2H]	10 mM
22	sodium chloride	natural abundance	50 mM
23	sodium azide	natural abundance	0.05 mM
24	magnesium chloride	natural abundance	5 mM

22 3D 13C-edited HMQC-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
25	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
26	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
27	TRIS	[U-2H]	10 mM
28	sodium chloride	natural abundance	50 mM
29	sodium azide	natural abundance	0.05 mM
30	magnesium chloride	natural abundance	5 mM

23 3D 13C-edited HMQC-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details The labeling is actually [U-13C;U-15N]-Gua+Cyt, but is not in the choice

#	Name	Isotope labeling	Concentration
31	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
32	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
33	TRIS	[U-2H]	10 mM
34	sodium chloride	natural abundance	50 mM
35	sodium azide	natural abundance	0.05 mM
36	magnesium chloride	natural abundance	5 mM

24 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.5 mM
8	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-13C; U-15N]	1.5 mM
9	TRIS	[U-2H]	10 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.05 mM
12	magnesium chloride	natural abundance	5 mM

25 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
19	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]	1.7 mM
20	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.7 mM
21	TRIS	[U-2H]	10 mM
22	sodium chloride	natural abundance	50 mM
23	sodium azide	natural abundance	0.05 mM
24	magnesium chloride	natural abundance	5 mM

26 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details The labeling is actually [U-13C;U-15N]-Gua+Cyt, but is not in the choice

#	Name	Isotope labeling	Concentration
31	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-13C; U-15N]-Gua	1.4 mM
32	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
33	TRIS	[U-2H]	10 mM
34	sodium chloride	natural abundance	50 mM
35	sodium azide	natural abundance	0.05 mM
36	magnesium chloride	natural abundance	5 mM

27 1D 15N-decoupled 1H watergate

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

28 1D 15N-decoupled 1H watergate

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

29 1D 15N-filtered 1H watergate

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

30 1D 15N-filtered 1H watergate

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

31 1D 15N-edited 1H watergate

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	natural abundance	1.3 ~ 2.2 mM
2	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	1.3 ~ 2.2 mM
3	TRIS	[U-2H]	10 mM
4	sodium chloride	natural abundance	50 mM
5	sodium azide	natural abundance	0.05 mM
6	magnesium chloride	natural abundance	5 mM

32 1D 15N-edited 1H watergate

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
13	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	1.4 mM
14	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	natural abundance	1.4 mM
15	TRIS	[U-2H]	10 mM
16	sodium chloride	natural abundance	50 mM
17	sodium azide	natural abundance	0.05 mM
18	magnesium chloride	natural abundance	5 mM

33 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
61	RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3')	[U-15N]	0.2 ~ 0.3 mM
62	RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3')	[U-15N]	0.2 ~ 0.3 mM
63	TRIS	[U-2H]	10 mM
64	sodium chloride	natural abundance	50 mM
65	sodium azide	natural abundance	0.05 mM
66	magnesium chloride	natural abundance	5 mM
67	Pf1 phage	natural abundance	14.6-20.5 mg/mL

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_19662_2mi0.nef
Input source #2: Coordindates	2mi0.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--------20--
GAGCAGCAUCGUCGGCUGCUCA
||||||||||||||||||||||
GAGCAGCAUCGUCGGCUGCUCA

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

-------110-------120-
GCGGCAGUUGACUACUGUCGC
|||||||||||||||||||||
GCGGCAGUUGACUACUGUCGC
--------10--------20-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	22	0	0	100.0
B	B	21	0	0	100.0

Content subtype: combined_19662_2mi0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	484		100.0 (chain: A, length: 22), 100.0 (chain: B, length: 21)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	86 (1)	noe	68.2 (chain: A, length: 22), 81.0 (chain: B, length: 21)
2	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	571 (1)	noe	100.0 (chain: A, length: 22), 100.0 (chain: B, length: 21)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	32 (1)	hbond	68.2 (chain: A, length: 22), 81.0 (chain: B, length: 21)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	173 (173)	.	77.3 (chain: A, length: 22), 85.7 (chain: B, length: 21)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	OK	16 (16)	.	36.4 (chain: A, length: 22), 38.1 (chain: B, length: 21)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%

--------10--------20--
GAGCAGCAUCGUCGGCUGCUCA
||||||||||||||||||||||
GAGCAGCAUCGUCGGCUGCUCA

Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%

-------110-------120-
GCGGCAGUUGACUACUGUCGC
|||||||||||||||||||||
GCGGCAGUUGACUACUGUCGC

Total number of assignments
- ¹H chemical shifts: 231
- ¹³C chemical shifts: 186
- ¹⁵N chemical shifts: 67

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	N7	231.521
1	G	N9	169.854
2	A	N1	220.82
2	A	N3	212.38
2	A	N7	228.17
2	A	N9	170.79
3	G	N7	233.358
3	G	N9	169.651
4	C	N3	196.862
4	C	N4	98.428
5	A	N1	220.15
5	A	N3	213.866
5	A	N7	230.305
5	A	N9	170.792
6	G	N7	233.352
6	G	N9	169.079
7	C	N4	98.472
10	C	N4	95.777
11	G	N7	228.298
11	G	N9	169.222
13	C	N4	98.758
16	C	N3	196.771
16	C	N4	98.877
18	G	N7	233.431
18	G	N9	169.841
19	C	N3	196.922
19	C	N4	99.382
21	C	N3	196.304
21	C	N4	97.595
22	A	N1	225.354
22	A	N3	215.577
22	A	N7	230.811
22	A	N9	171.166

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	194	116	59.8
¹³C chemical shifts	147	92	62.6
¹⁵N chemical shifts	11	8	72.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	58	43.9
¹³C chemical shifts	110	56	50.9

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	58	93.5
¹³C chemical shifts	37	36	97.3
¹⁵N chemical shifts	11	8	72.7

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	15	15	100.0
¹³C chemical shifts	15	15	100.0

Entity_assemble_ID: B

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
102	C	N3	197.033
102	C	N4	97.922
105	C	N3	196.498
105	C	N4	98.924
106	A	N1	219.701
106	A	N3	214.366
111	A	N1	223.773
111	A	N3	212.377
111	A	N7	221.528
112	C	N4	97.264
114	A	N1	225.734
114	A	N3	217.878
114	A	N7	233.53
115	C	N3	197.247
115	C	N4	98.021
119	C	N3	196.232
119	C	N4	98.315
121	C	N4	97.539

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	185	115	62.2
¹³C chemical shifts	140	94	67.1
¹⁵N chemical shifts	12	8	66.7

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	126	60	47.6
¹³C chemical shifts	105	59	56.2

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	55	93.2
¹³C chemical shifts	35	35	100.0
¹⁵N chemical shifts	12	8	66.7

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	13	13	100.0
¹³C chemical shifts	13	13	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 68.2%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 81.0%
- Total number of restraints: 86
- Weight of restraints: 1.0 (86)
- Potential type of restraints: square-well-parabolic (86)
- Range of distance target values: 1.87, 6.7 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_6
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 100.0%
  - Total number of restraints: 568
  - Weight of restraints: 1.0 (568)
  - Potential type of restraints: square-well-parabolic (568)
  - Range of distance target values: 2.0, 29.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 68.2%
      - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 81.0%
    - Total number of restraints: 32
    - Weight of restraints: 1.0 (32)
    - Potential type of restraints: square-well-parabolic (32)
    - Range of distance target values: 3.5, 12.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 77.3%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 85.7%
- Total number of restraints: 173
- Total number of restraints per polymer type: 173
- Weight of restraints: 1.0 (173)
- Potential type of restraints: square-well-parabolic (173)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 36.4%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 38.1%
- Total number of restraints: 16
- Potential type of restraints: undefined (16)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords kissing-loop interaction, Neurospora VS ribozyme, NMR structural studies, substrate recognition, U-turn

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Found 1 Document (0.365 seconds)

BMRB: 19662

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Sample #11

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

Related entities 2. RNA (5'-R(*GP*CP*GP*GP*CP*AP*GP*UP*UP*GP*AP*CP*UP*AP*CP*UP*GP*UP*CP*GP*C)-3'), : 1 entities Detail

Experiments performed 33 experiments Detail

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Related entities 1. RNA (5'-R(GPAPGPCPAPGPCPAPUPCPGPUPCPGPGPCPUPGPCPUPCPA)-3'), : 1 entities Detail

Related entities 2. RNA (5'-R(GPCPGPGPCPAPGPUPUPGPAPCPUPAPCPUPGPUPCPGP*C)-3'), : 1 entities Detail