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BMRB: 30026

5IEM

NMR structure of the 5'-terminal hairpin of the 7SK snRNA

Authors

Bourbigot, S., Dock-Bregeon, A., Coutant, J., Kieffer, B., Lebars, I.

Assembly

5'-terminal hairpin of the 7SK snRNA

Entity

1. 5'-terminal hairpin of the 7SK snRNA (polymer, Thiol state: not present), 57 monomers, 18331.75 Da Detail

GGGAUCUGUC ACCCCAUUGA UCGCCUUCGG GCUGAUCUGG CUGGCUAGGC GGGUCCC

Formula weight

18331.75 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 37.8 %, Completeness (bb): 19.6 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	37.8 % (347 of 919)	50.6 % (256 of 506)	17.9 % (68 of 380)	69.7 % (23 of 33)
Suger, PO4	19.6 % (123 of 627)	30.4 % (104 of 342)	6.7 % (19 of 285)
Nucleobase	76.7 % (224 of 292)	92.7 % (152 of 164)	51.6 % (49 of 95)	69.7 % (23 of 33)
Aromatic	76.6 % (196 of 256)	96.9 % (124 of 128)	51.6 % (49 of 95)	69.7 % (23 of 33)

1. RNA (57-MER)

GGGAUCUGUC ACCCCAUUGA UCGCCUUCGG GCUGAUCUGG CUGGCUAGGC GGGUCCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	HPI	natural abundance	0.8 mM
2	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
3	HPI	[U-13C; U-15N]-Ade	0.4 mM
4	HPI	[U-13C; U-15N]-Cyt	0.4 mM
5	HPI	[U-13C; U-15N]-Gua	0.4 mM
6	HPI	[U-13C; U-15N]-Ura	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	HPI	[U-13C; U-15N]-Ade	0.4 mM
17	HPI	[U-13C; U-15N]-Gua	0.4 mM
18	HPI	[U-13C; U-15N]-Ura	0.4 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

Release date

2016-10-27

Citation

Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA
Bourbigot, S., Dock-Bregeon, A., Eberling, P., Coutant, J., Kieffer, B., Lebars, I.
RNA (2016), 22, 1844-1858, PubMed 27852926 , DOI 10.1261/rna.056523.116 , Abstract

Experiments performed 12 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 288 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	HPI	natural abundance	0.8 mM
2	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
3	HPI	[U-13C; U-15N]-Ade	0.4 mM
4	HPI	[U-13C; U-15N]-Cyt	0.4 mM
5	HPI	[U-13C; U-15N]-Gua	0.4 mM
6	HPI	[U-13C; U-15N]-Ura	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

2 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 288 K, pH 6.4

#	Name	Isotope labeling	Concentration
1	HPI	natural abundance	0.8 mM
2	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
3	HPI	[U-13C; U-15N]-Ade	0.4 mM
4	HPI	[U-13C; U-15N]-Cyt	0.4 mM
5	HPI	[U-13C; U-15N]-Gua	0.4 mM
6	HPI	[U-13C; U-15N]-Ura	0.4 mM
7	H2O	natural abundance	90 %
8	D2O	natural abundance	10 %

3 2D 1H-1H NOESY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

4 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

5 2D 1H-13C HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	HPI	[U-13C; U-15N]-Ade	0.4 mM
17	HPI	[U-13C; U-15N]-Gua	0.4 mM
18	HPI	[U-13C; U-15N]-Ura	0.4 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

6 2D 1H-1H TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

7 2D DQF-COSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

8 3D HCCH-TOCSY

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

9 2D 1H-15N HSQC

Instrument

Bruker AvanceIII - 700 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
16	HPI	[U-13C; U-15N]-Ade	0.4 mM
17	HPI	[U-13C; U-15N]-Gua	0.4 mM
18	HPI	[U-13C; U-15N]-Ura	0.4 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

10 3D HCP

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

11 2D HPCOSY

Instrument

Bruker AvanceIII - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

12 2D HCN

Instrument

Bruker AvanceIII - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 101325 Pa, Temperature 303 K, pH 6.4

#	Name	Isotope labeling	Concentration
9	HPI	natural abundance	0.8 mM
10	HPI	[U-99% 13C; U-99% 15N]	0.4 mM
11	HPI	[U-13C; U-15N]-Ade	0.4 mM
12	HPI	[U-13C; U-15N]-Cyt	0.4 mM
13	HPI	[U-13C; U-15N]-Gua	0.4 mM
14	HPI	[U-13C; U-15N]-Ura	0.4 mM
15	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_30026_5iem.nef
Input source #2: Coordindates	5iem.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--------30--------40--------50-------
GGGAUCUGUCACCCCAUUGAUCGCCUUCGGGCUGAUCUGGCUGGCUAGGCGGGUCCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GGGAUCUGUCACCCCAUUGAUCGCCUUCGGGCUGAUCUGGCUGGCUAGGCGGGUCCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	57	0	0	100.0

Content subtype: combined_30026_5iem.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	347		100.0 (chain: A, length: 57)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	762 (1)	noe	100.0 (chain: A, length: 57)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	118 (1)	hbond	77.2 (chain: A, length: 57)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	483 (483)	.	100.0 (chain: A, length: 57)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	44 (44)	.	49.1 (chain: A, length: 57)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 256
  - ¹³C chemical shifts: 68
  - ¹⁵N chemical shifts: 23
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	506	256	50.6
¹³C chemical shifts	380	68	17.9
¹⁵N chemical shifts	33	23	69.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	342	104	30.4
¹³C chemical shifts	285	19	6.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	164	152	92.7
¹³C chemical shifts	95	49	51.6
¹⁵N chemical shifts	33	23	69.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	31	100.0
¹³C chemical shifts	31	31	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 100.0%
- Total number of restraints: 762
- Weight of restraints: 1.0 (762)
- Potential type of restraints: square-well-parabolic (762)
- Range of distance target values: 2.0, 5.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 77.2%
  - Total number of restraints: 118
  - Weight of restraints: 1.0 (118)
  - Potential type of restraints: square-well-parabolic (118)
  - Range of distance target values: 1.85, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 100.0%
- Total number of restraints: 483
- Total number of restraints per polymer type: 483
- Weight of restraints: 1.0 (483)
- Potential type of restraints: square-well-parabolic (483)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 49.1%
- Total number of restraints: 44
- Potential type of restraints: undefined (44)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords RNA, regulator, transcription

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Found 1 Document (0.384 seconds)

BMRB: 30026

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Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail