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BMRB: 17088

2KYE

Solution structure of the pseudouridine modified P6.1 hairpin of human telomerase RNA

Authors

Kim, N., Theimer, C.A., Mitchell, J.R., Collins, K., Feigon, J.

Assembly

P6.1 hairpin

Entity

1. P6.1 hairpin (polymer, Thiol state: not present), 15 monomers, 4887.869 Da Detail

GAGAGXXGGG CXCXC

Formula weight

4887.869 Da

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 73.3 %, Completeness: 100.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	100.0 % (171 of 171)	100.0 % (94 of 94)	100.0 % (71 of 71)	100.0 % (6 of 6)
Suger, PO4	100.0 % (121 of 121)	100.0 % (66 of 66)	100.0 % (55 of 55)
Nucleobase	100.0 % (50 of 50)	100.0 % (28 of 28)	100.0 % (16 of 16)	100.0 % (6 of 6)
Aromatic	100.0 % (44 of 44)	100.0 % (22 of 22)	100.0 % (16 of 16)	100.0 % (6 of 6)

1. RNA

GAGAGXXGGG CXCXC

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA	natural abundance		0.6 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	RNA	natural abundance		0.6 mM
5	D2O	natural abundance		100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
6	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
9	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
10	D2O	natural abundance		100 %

Release date

2010-08-17

Citation

Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA
Kim, N., Theimer, C.A., Mitchell, J.R., Collins, K., Feigon, J.
Nucleic Acids Res. (2010), 38, 6746-6756, PubMed 20554853 , DOI 10.1093/nar/gkq525 , Abstract

Related entities 1. P6.1 hairpin, : 1 : 12 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
6	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	RNA	natural abundance		0.6 mM
5	D2O	natural abundance		100 %

3 2D 1H-13C HSQC

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
9	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
10	D2O	natural abundance		100 %

4 2D 1H-1H COSY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
9	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
10	D2O	natural abundance		100 %

5 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA	natural abundance		0.6 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

6 2D 1H-1H NOESY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	RNA	natural abundance		0.6 mM
5	D2O	natural abundance		100 %

7 2D 1H-1H Filter/Edited NOESY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
9	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
10	D2O	natural abundance		100 %

8 3D HCCH-TOCSY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8, Details A,C,G 13C,15N labeled

#	Name	Isotope labeling	Type	Concentration
9	RNA	[U-98% 13C; U-98% 15N]		0.8 mM
10	D2O	natural abundance		100 %

9 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 283 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	RNA	natural abundance		0.6 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

10 2D 1H-1H TOCSY

Instrument

Bruker DRX - 500 MHz No cryoprobe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
4	RNA	natural abundance		0.6 mM
5	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_17088_2kye.nef
Input source #2: Coordindates	2kye.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:5:G:O3'	1:6:PSU:P	unknown	unknown	n/a
1:6:PSU:O3'	1:7:PSU:P	unknown	unknown	n/a
1:7:PSU:O3'	1:8:G:P	unknown	unknown	n/a
1:11:C:O3'	1:12:PSU:P	unknown	unknown	n/a
1:12:PSU:O3'	1:13:C:P	unknown	unknown	n/a
1:13:C:O3'	1:14:PSU:P	unknown	unknown	n/a
1:14:PSU:O3'	1:15:C:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, RDC restraints, Coordinates
A	7	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates
A	12	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, RDC restraints, Coordinates
A	14	PSU	PSEUDOURIDINE-5'-MONOPHOSPHATE	Assigned chemical shifts, Distance restraints, Torsion angle restraints, RDC restraints, Coordinates

Sequence alignments

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

--------10-----
GAGAGXXGGGCXCXC
|||||||||||||||
GAGAGXXGGGCXCXC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	15	0	0	100.0

Content subtype: combined_17088_2kye.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	7		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	245		100.0 (chain: A, length: 15)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	273 (1)	noe	100.0 (chain: A, length: 15)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	27 (1)	hbond	80.0 (chain: A, length: 15)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	89 (89)	.	100.0 (chain: A, length: 15)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	27 (27)	.	93.3 (chain: A, length: 15)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 138
- ¹³C chemical shifts: 91
- ¹⁵N chemical shifts: 16

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	A	H61	7.317
2	A	H62	6.815
2	A	N6	81.39
3	G	H21	7.996
3	G	H22	6.035
3	G	N2	74.61
4	A	H61	7.314
4	A	H62	6.86
4	A	N6	82.35
5	G	H21	8.511
5	G	H22	6.461
5	G	N2	75.12
8	G	N2	73.88
9	G	H22	6.397
9	G	N2	72.7
10	G	H22	6.46
10	G	N2	73.72
11	C	N4	97.81
13	C	N4	96.89
15	C	N4	96.17

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	142	128	90.1
¹³C chemical shifts	107	91	85.0
¹⁵N chemical shifts	14	6	42.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	90	95.7
¹³C chemical shifts	75	71	94.7

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	38	79.2
¹³C chemical shifts	32	20	62.5
¹⁵N chemical shifts	14	6	42.9

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	10	10	100.0
¹³C chemical shifts	10	10	100.0

Histogram of normalized assigned chemical shifts

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 273
- Weight of restraints: 1.0 (273)
- Potential type of restraints: square-well-parabolic (273)
- Range of distance target values: 2.65, 6.5 (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_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 80.0%
  - Total number of restraints: 27
  - Weight of restraints: 1.0 (27)
  - Potential type of restraints: square-well-parabolic (27)
  - Range of distance target values: 1.89, 2.95 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 15, Sequence coverage: 100.0%
- Total number of restraints: 89
- Total number of restraints per polymer type: 89
- Weight of restraints: 1.0 (89)
- Potential type of restraints: square-well-parabolic (89)
- 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: 15, Sequence coverage: 93.3%
- Total number of restraints: 27
- Potential type of restraints: square-well-parabolic (27)
- Range of observed RDC values: -9.45, 7.64 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Hairpin, NMR, Pseudouridine, RNA, Structure, Telomerase, hairpin, P6.1, pseudouridine, telomerase