BMRBj - BMREntryMaster

Found 1 Document (0.273 seconds)

BMRB: 30730

6VZC

Tandem UU:GA mismatch within an RNA helix

Authors

Nikonowicz, E.P., Chang, A.T.

Assembly

RNA 28-mer

Entity

1. RNA 28-mer (polymer, Thiol state: not present), 28 monomers, 9026.303 Da Detail

GGGCUGUGAU GCUUCGGCAU AUCAGCCC

Formula weight

9026.303 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 96.0 %, Completeness (bb): 97.4 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	96.0 % (432 of 450)	96.8 % (239 of 247)	96.8 % (181 of 187)	75.0 % (12 of 16)
Suger, PO4	97.4 % (300 of 308)	98.8 % (166 of 168)	95.7 % (134 of 140)
Nucleobase	93.0 % (132 of 142)	92.4 % (73 of 79)	100.0 % (47 of 47)	75.0 % (12 of 16)
Aromatic	93.7 % (118 of 126)	93.7 % (59 of 63)	100.0 % (47 of 47)	75.0 % (12 of 16)

1. entity 1

GGGCUGUGAU GCUUCGGCAU AUCAGCCC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.5 mM RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	RNA	natural abundance		1.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.3 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	RNA	[U-99% 13C; U-99% 15N]		1.3 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 0.25 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	RNA	[U-99% 13C; U-99% 15N]		0.25 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.4 mM [U-99% 13C; U-99% 15N] RNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-99% 13C; U-99% 15N]		1.4 mM

Release date

2020-05-05

Citation

2-Amino-1,3-benzothiazole-6-carboxamide Preferentially Binds the Tandem Mismatch Motif r(UY:GA)
Chang, A.T., Chen, L., Song, L., Zhang, S., Nikonowicz, E.P.
Biochemistry (2020), 59, 3225-3234, PubMed 32786414 , DOI 10.1021/acs.biochem.0c00369 , Abstract

Related entities 1. RNA 28-mer, : 1 : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.5 mM RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	RNA	natural abundance		1.5 mM

2 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.3 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	RNA	[U-99% 13C; U-99% 15N]		1.3 mM

3 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.3 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	RNA	[U-99% 13C; U-99% 15N]		1.3 mM

4 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.3 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	RNA	[U-99% 13C; U-99% 15N]		1.3 mM

5 2D 1H-13C ct-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 0.25 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
3	RNA	[U-99% 13C; U-99% 15N]		0.25 mM

6 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 6.8 (±0.1), Details 1.4 mM [U-99% 13C; U-99% 15N] RNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-99% 13C; U-99% 15N]		1.4 mM

7 2D 1H-13C ctep-HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.3 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	RNA	[U-99% 13C; U-99% 15N]		1.3 mM

8 2d H(CN)C

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 299 K, pH 6.8 (±0.1), Details 1.3 mM [U-99% 13C; U-99% 15N] RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
2	RNA	[U-99% 13C; U-99% 15N]		1.3 mM

9 2D H(N)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 6.8 (±0.1), Details 1.4 mM [U-99% 13C; U-99% 15N] RNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-99% 13C; U-99% 15N]		1.4 mM

10 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 285 K, pH 6.8 (±0.1), Details 1.5 mM RNA, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	RNA	natural abundance		1.5 mM

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 285 K, pH 6.8 (±0.1), Details 1.4 mM [U-99% 13C; U-99% 15N] RNA, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
4	RNA	[U-99% 13C; U-99% 15N]		1.4 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30730_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: bmr30730_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	505		100.0 (chain: 1, length: 28)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 28, Sequence coverage: 100.0%

--------10--------20--------
GGGCUGUGAUGCUUCGGCAUAUCAGCCC
||||||||||||||||||||||||||||
GGGCUGUGAUGCUUCGGCAUAUCAGCCC

Total number of assignments
- ¹H chemical shifts: 239
- ¹³C chemical shifts: 215
- ¹⁵N chemical shifts: 51

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	C2	156.67
2	G	C6	161.79
2	G	N7	234.48
2	G	N9	170.41
3	G	C2	157.12
3	G	C6	161.9
3	G	N7	234.78
3	G	N9	169.54
4	C	C2	159.29
4	C	C4	161.9
4	C	N4	97.52
5	U	C2	152.92
5	U	C4	169.7
6	G	C2	156.21
6	G	C6	161.67
6	G	N7	237.0
6	G	N9	170.51
7	U	C2	154.27
7	U	C4	166.87
8	G	C2	160.2
8	G	N7	231.41
8	G	N9	172.44
9	A	N1	223.94
9	A	N3	215.04
9	A	N7	231.37
9	A	N9	169.47
10	U	C2	152.87
11	G	C2	156.69
11	G	C6	161.54
11	G	N7	235.3
11	G	N9	170.58
12	C	C2	158.9
12	C	N4	99.25
13	U	C2	153.31
14	U	C2	155.3
15	C	C2	160.3
16	G	C2	155.86
16	G	C6	161.77
16	G	N7	237.68
16	G	N9	167.46
17	G	C2	155.86
17	G	C6	162.6
17	G	N7	233.81
17	G	N9	171.1
18	C	C2	159.11
18	C	N4	97.45
19	A	N1	223.83
19	A	N3	214.37
19	A	N7	231.81
19	A	N9	171.55
20	U	C2	153.36
21	A	N1	226.24
21	A	N3	216.3
21	A	N7	231.89
21	A	N9	169.69
22	U	C2	152.25
22	U	C4	168.23
23	C	C2	159.35
23	C	N4	97.81
24	A	N1	220.75
24	A	N3	213.85
24	A	N7	231.22
24	A	N9	170.8
25	G	C2	157.27
25	G	C6	161.67
25	G	N7	234.63
25	G	N9	169.76
26	C	C2	159.11
26	C	N4	98.49
27	C	C2	159.29
27	C	N4	98.29
28	C	C2	160.22
28	C	N4	96.92

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	247	239	96.8
¹³C chemical shifts	187	181	96.8
¹⁵N chemical shifts	16	12	75.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	168	166	98.8
¹³C chemical shifts	140	134	95.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	73	92.4
¹³C chemical shifts	47	47	100.0
¹⁵N chemical shifts	16	12	75.0

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	17	17	100.0
¹³C chemical shifts	17	17	100.0

Histogram of normalized assigned chemical shifts

Keywords GA base pair, RNA, UU base pair, internal loop, mismatch, structural motif

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Found 1 Document (0.273 seconds)

BMRB: 30730

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. RNA 28-mer, : 1 : 1 entities Detail

Experiments performed 11 experiments Detail

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Chemical shift validation 3 contents Detail