BMRBj - BMREntryMaster

Found 1 Document (0.33 seconds)

BMRB: 34100

5N5C

NMR solution structure of the TSL2 RNA hairpin

Authors

Garcia-Lopez, A., Wacker, A., Tessaro, F., Jonker, H.R.A., Richter, C., Comte, A., Berntenis, N., Schmucki, R., Hatje, K., Sciarra, D., Konieczny, P., Fournet, G., Faustino, I., Orozco, M., Artero, R., Goekjian, P., Metzger, F., Ebeling, M., Joseph, B., Schwalbe, H., Scapozza, L.

Assembly

RNA (19-MER)

Entity

1. RNA (19-MER) (polymer, Thiol state: not present), 19 monomers, 6111.596 Da Detail

AUUCCUUAAA UUAAGGAGU

Formula weight

6111.596 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.6 %, Completeness (bb): 67.9 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	69.6 % (211 of 303)	85.9 % (140 of 163)	51.5 % (67 of 130)	40.0 % (4 of 10)
Suger, PO4	67.9 % (142 of 209)	85.1 % (97 of 114)	47.4 % (45 of 95)
Nucleobase	73.4 % (69 of 94)	87.8 % (43 of 49)	62.9 % (22 of 35)	40.0 % (4 of 10)
Aromatic	72.2 % (65 of 90)	86.7 % (39 of 45)	62.9 % (22 of 35)	40.0 % (4 of 10)

1. entity 1

AUUCCUUAAA UUAAGGAGU

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.1 mM
2	RNA (19-MER)	natural abundance	0.6 mM
3	sodium phosphate	natural abundance	50 mM

Sample #2

Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
4	EDTA	natural abundance	0.1 mM
5	RNA (19-MER)	natural abundance	0.6 mM
6	sodium phosphate	natural abundance	50 mM

Sample #3

Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM [U-98% 13C; U-96-98% 15N]-ADE RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

Release date

2017-02-15

Citation

Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes
Garcia-Lopez, A., Tessaro, F., Jonker, H., Wacker, A., Richter, C., Comte, A., Berntenis, N., Schmucki, R., Hatje, K., Petermann, O., Chiriano, G., Perozzo, R., Sciarra, D., Konieczny, P., Faustino, I., Fournet, G., Orozco, M., Artero, R., Metzger, F., Ebeling, M., Goekjian, P., Joseph, B., Schwalbe, H., Scapozza, L.
Nat. Commun. (2018), 9, 2032-2032, PubMed 29795225 , DOI 10.1038/s41467-018-04110-1 , Abstract

Related entities 1. RNA (19-MER), : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
4	EDTA	natural abundance	0.1 mM
5	RNA (19-MER)	natural abundance	0.6 mM
6	sodium phosphate	natural abundance	50 mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.1 mM
2	RNA (19-MER)	natural abundance	0.6 mM
3	sodium phosphate	natural abundance	50 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.1 mM
2	RNA (19-MER)	natural abundance	0.6 mM
3	sodium phosphate	natural abundance	50 mM

4 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM [U-98% 13C; U-96-98% 15N]-ADE RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

5 2D 12C-filtered 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

6 2D 13C-editted 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

7 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
4	EDTA	natural abundance	0.1 mM
5	RNA (19-MER)	natural abundance	0.6 mM
6	sodium phosphate	natural abundance	50 mM

8 2D 1H-1H COSY

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
4	EDTA	natural abundance	0.1 mM
5	RNA (19-MER)	natural abundance	0.6 mM
6	sodium phosphate	natural abundance	50 mM

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 99.8% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 99.8% D2O

#	Name	Isotope labeling	Concentration
4	EDTA	natural abundance	0.1 mM
5	RNA (19-MER)	natural abundance	0.6 mM
6	sodium phosphate	natural abundance	50 mM

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

11 2D 1H-13C HSQC sugar

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

12 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.4, Details 0.6 mM RNA (19-MER), 50 mM sodium phosphate, 0.1 mM EDTA, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	EDTA	natural abundance	0.1 mM
2	RNA (19-MER)	natural abundance	0.6 mM
3	sodium phosphate	natural abundance	50 mM

13 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	EDTA	natural abundance	0.1 mM
8	RNA (19-MER)	[U-98% 13C; U-96-98% 15N]-ADE	0.6 mM
9	sodium phosphate	natural abundance	50 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34100_5n5c.nef
Input source #2: Coordindates	5n5c.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---------
AUUCCUUAAAUUAAGGAGU
|||||||||||||||||||
AUUCCUUAAAUUAAGGAGU

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	19	0	0	100.0

Content subtype: combined_34100_5n5c.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	221		100.0 (chain: A, length: 19)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	458 (1)	noe	100.0 (chain: A, length: 19)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 150
  - ¹³C chemical shifts: 67
  - ¹⁵N chemical shifts: 4
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	A	H61	5.67
10	A	H62	5.67
13	A	H61	7.11
13	A	H62	7.11
14	A	H62	7.5
14	A	H61	6.16
15	G	H22	7.96
15	G	H21	5.77
16	G	H21	7.7
16	G	H22	7.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	163	140	85.9
¹³C chemical shifts	130	67	51.5
¹⁵N chemical shifts	10	4	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	97	85.1
¹³C chemical shifts	95	45	47.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	43	87.8
¹³C chemical shifts	35	22	62.9
¹⁵N chemical shifts	10	4	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	15	88.2

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 19, Sequence coverage: 100.0%
- Total number of restraints: 458
- Weight of restraints: 1.0 (458)
- Potential type of restraints: square-well-parabolic (458)
- Range of distance target values: 1.74, 4.25 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords RNA, Terminal Stem-Loop 2 Survival Motor Neuron

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Found 1 Document (0.33 seconds)

BMRB: 34100

Sample #1

Sample #2

Sample #3

Related entities 1. RNA (19-MER), : 1 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 3 contents Detail