BMRBj - BMREntryMaster

Found 1 Document (0.366 seconds)

BMRB: 17860

2LHP

high resolution NMR solution structure of helix H1 of the chimpanzee HAR1 RNA

Authors

Cevec, M., Ziegeler, M., Richter, C., Schwalbe, H.

Assembly

RNA (37-MER)

Entity

1. RNA (37-MER) (polymer, Thiol state: not present), 37 monomers, 11935.05 Da Detail

GGGUGAAAUG GAGGACUUCG GUCCUCAAAU UUCACCC

Formula weight

11935.05 Da

Source organism

Pan troglodytes

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 77.4 %, Completeness (bb): 68.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H
All	77.4 % (250 of 323)	77.4 % (250 of 323)
Suger, PO4	68.5 % (152 of 222)	68.5 % (152 of 222)
Nucleobase	97.0 % (98 of 101)	97.0 % (98 of 101)
Aromatic	96.4 % (80 of 83)	96.4 % (80 of 83)

1. RNA (37-MER)

GGGUGAAAUG GAGGACUUCG GUCCUCAAAU UUCACCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (37-MER)	natural abundance	0.6 mM
2	potassium chloride	natural abundance	50 mM
3	potassium phosphate	natural abundance	25 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
4	RNA (37-MER)	[U-100% 15N]	0.4 mM
5	potassium chloride	natural abundance	50 mM
6	potassium phosphate	natural abundance	25 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	RNA (37-MER)	[U-13C; U-15N]-Ade,Ura	0.3 mM
8	potassium chloride	natural abundance	50 mM
9	potassium phosphate	natural abundance	25 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
10	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
11	potassium chloride	natural abundance	50 mM
12	potassium phosphate	natural abundance	25 mM

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

Release date

2012-07-23

Citation

NMR studies of HAR1 RNA secondary structures reveal conformational dynamics in the human RNA
Ziegeler, M., Cevec, M., Richter, C., Schwalbe, H.
Chembiochem. (2012), 13, 2100-2112, PubMed 22961937 , DOI 10.1002/cbic.201200401 , Abstract

Related entities 1. RNA (37-MER), : 1 : 1 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Concentration
4	RNA (37-MER)	[U-100% 15N]	0.4 mM
5	potassium chloride	natural abundance	50 mM
6	potassium phosphate	natural abundance	25 mM

2 2D HNN-COSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Concentration
4	RNA (37-MER)	[U-100% 15N]	0.4 mM
5	potassium chloride	natural abundance	50 mM
6	potassium phosphate	natural abundance	25 mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (37-MER)	natural abundance	0.6 mM
2	potassium chloride	natural abundance	50 mM
3	potassium phosphate	natural abundance	25 mM

4 3D 1H-13C-13C-TROSY relayed HCCH-COSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
10	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
11	potassium chloride	natural abundance	50 mM
12	potassium phosphate	natural abundance	25 mM

5 2D 1H-13C HSQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (37-MER)	natural abundance	0.6 mM
2	potassium chloride	natural abundance	50 mM
3	potassium phosphate	natural abundance	25 mM

7 2D DQF-COSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (37-MER)	natural abundance	0.6 mM
2	potassium chloride	natural abundance	50 mM
3	potassium phosphate	natural abundance	25 mM

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

9 2D 1H-13C HCCNH-TOCSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	RNA (37-MER)	[U-13C; U-15N]-Ade,Ura	0.3 mM
8	potassium chloride	natural abundance	50 mM
9	potassium phosphate	natural abundance	25 mM

10 3D HCP

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

11 2D 1H-31P COSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

12 3D forward-directed HCC-TOCSY-CCH E.COSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

13 2D H(C)N

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

14 2D HNCO

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 6.2

#	Name	Isotope labeling	Concentration
10	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
11	potassium chloride	natural abundance	50 mM
12	potassium phosphate	natural abundance	25 mM

15 3D HCCH-TOCSY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
13	RNA (37-MER)	[U-13C; U-15N]-Cyt,Gua	1 mM
14	potassium chloride	natural abundance	50 mM
15	potassium phosphate	natural abundance	25 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17860_2lhp.nef
Input source #2: Coordindates	2lhp.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-------
GGGUGAAAUGGAGGACUUCGGUCCUCAAAUUUCACCC
|||||||||||||||||||||||||||||||||||||
GGGUGAAAUGGAGGACUUCGGUCCUCAAAUUUCACCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	37	0	0	100.0

Content subtype: combined_17860_2lhp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	282		100.0 (chain: A, length: 37)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	327 (1)	noe	100.0 (chain: A, length: 37)
2	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	400 (1)	noe	100.0 (chain: A, length: 37)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	80 (1)	hbond	86.5 (chain: A, length: 37)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	269 (269)	.	97.3 (chain: A, length: 37)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	89 (89)	.	91.9 (chain: A, length: 37)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%

--------10--------20--------30-------
GGGUGAAAUGGAGGACUUCGGUCCUCAAAUUUCACCC
|||||||||||||||||||||||||||||||||||||
GGGUGAAAUGGAGGACUUCGGUCCUCAAAUUUCACCC

Total number of assignments
- ¹H chemical shifts: 282

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	H22	6.05
3	G	H21	8.475
3	G	H22	6.076
3	G	HO2'	7.031
6	A	H61	7.753
6	A	H62	6.649
7	A	H61	7.969
7	A	H62	6.728
7	A	HO2'	6.835
8	A	H61	8.046
8	A	H62	6.639
11	G	H21	7.695
11	G	H22	5.828
13	G	H21	8.316
13	G	H22	6.077
14	G	H22	5.849
15	A	H61	8.451
15	A	H62	6.68
15	A	HO2'	6.939
16	C	HO2'	7.033
17	U	HO2'	6.77
21	G	H21	8.882
21	G	H22	6.718
21	G	HO2'	6.887
23	C	HO2'	6.886
24	C	HO2'	6.752
33	C	HO2'	6.626
34	A	H61	7.996
34	A	H62	6.37
34	A	HO2'	7.018
35	C	HO2'	6.861
36	C	HO2'	6.868

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	250	77.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	152	68.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	98	97.0

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	28	28	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
- Total number of restraints: 327
- Weight of restraints: 1.0 (327)
- Potential type of restraints: square-well-parabolic (327)
- Range of distance target values: 2.3, 4.4 (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_7
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 100.0%
  - Total number of restraints: 400
  - Weight of restraints: 1.0 (400)
  - Potential type of restraints: square-well-parabolic (400)
  - Range of distance target values: 1.93, 4.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 86.5%
    - Total number of restraints: 80
    - Weight of restraints: 1.0 (80)
    - Potential type of restraints: square-well-parabolic (80)
    - Range of distance target values: 1.61, 3.0 (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: 37, Sequence coverage: 97.3%
- Total number of restraints: 269
- Total number of restraints per polymer type: 269
- Weight of restraints: 1.0 (269)
- Potential type of restraints: square-well-parabolic (269)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 37, Sequence coverage: 91.9%
- Total number of restraints: 89
- Potential type of restraints: undefined (89)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords 37-nt hairpin, chimpanzee HAR1 RNA, UUCG tetraloop

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Found 1 Document (0.366 seconds)

BMRB: 17860

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Sample #5

Related entities 1. RNA (37-MER), : 1 : 1 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 7 contents Detail