BMRBj - BMREntryMaster

Found 1 Document (0.351 seconds)

BMRB: 19260

2M8K

A pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo

Authors

Cash, D.D., Cohen, O., Kim, N., Shefer, K., Brown, Y., Ulyanov, N.B., Tzfati, Y., Feigon, J.

Assembly

RNA (48-MER)

Entity

1. RNA (48-MER) (polymer, Thiol state: not present), 48 monomers, 15215.83 Da Detail

GGUUUCUUUU UAGUGAUUUU UCCAAACCCC UUUGUGCAAA AAUCAUUA

Formula weight

15215.83 Da

Source organism

Kluyveromyces lactis

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 73.8 %, Completeness (bb): 66.7 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	73.8 % (576 of 780)	73.8 % (312 of 423)	74.8 % (247 of 330)	63.0 % (17 of 27)
Suger, PO4	66.7 % (352 of 528)	66.0 % (190 of 288)	67.5 % (162 of 240)
Nucleobase	88.9 % (224 of 252)	90.4 % (122 of 135)	94.4 % (85 of 90)	63.0 % (17 of 27)
Aromatic	90.6 % (212 of 234)	94.0 % (110 of 117)	94.4 % (85 of 90)	63.0 % (17 of 27)

1. RNA (48-MER)

GGUUUCUUUU UAGUGAUUUU UCCAAACCCC UUUGUGCAAA AAUCAUUA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	RNA_(48-MER)	natural abundance	1 mM
2	TRIS	natural abundance	10 mM
3	Magnesium Chloride	natural abundance	0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
6	RNA_(48-MER)	natural abundance	1 mM
7	TRIS	natural abundance	10 mM
8	Magnesium Chloride	natural abundance	0.5 mM
9	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
10	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
11	TRIS	natural abundance	10 mM
12	Magnesium Chloride	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
16	TRIS	natural abundance	10 mM
17	Magnesium Chloride	natural abundance	0.5 mM
18	D2O	natural abundance	100 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
19	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
20	TRIS	natural abundance	10 mM
21	Magnesium Chloride	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

Sample #6

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
24	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
25	TRIS	natural abundance	10 mM
26	Magnesium Chloride	natural abundance	0.5 mM
27	D2O	natural abundance	100 %

Sample #7

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
28	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri,Cyt,Gua	1 mM
29	TRIS	natural abundance	10 mM
30	Magnesium Chloride	natural abundance	0.5 mM
31	H2O	natural abundance	90 %
32	D2O	natural abundance	10 %

Release date

2013-06-16

Citation

Pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo
Cash, D.D., Cohen, O., Kim, N., Shefer, K., Brown, Y., Ulyanov, N.B., Tzfati, Y., Feigon, J.
Proc. Natl. Acad. Sci. U. S. A. (2013), 110, 10970-10975, PubMed 23776224 , DOI 10.1073/pnas.1309590110 , Abstract

Related entities 1. RNA (48-MER), : 1 entities Detail

Experiments performed 16 experiments Detail

1 2D 11echo NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	RNA_(48-MER)	natural abundance	1 mM
2	TRIS	natural abundance	10 mM
3	Magnesium Chloride	natural abundance	0.5 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 13C Filtered/Edited NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
16	TRIS	natural abundance	10 mM
17	Magnesium Chloride	natural abundance	0.5 mM
18	D2O	natural abundance	100 %

3 2D 13C Filtered/Edited NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
24	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
25	TRIS	natural abundance	10 mM
26	Magnesium Chloride	natural abundance	0.5 mM
27	D2O	natural abundance	100 %

4 2D NOESY presat

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
6	RNA_(48-MER)	natural abundance	1 mM
7	TRIS	natural abundance	10 mM
8	Magnesium Chloride	natural abundance	0.5 mM
9	D2O	natural abundance	100 %

5 2D HCCH-COSY, 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
16	TRIS	natural abundance	10 mM
17	Magnesium Chloride	natural abundance	0.5 mM
18	D2O	natural abundance	100 %

6 2D HCCH COSY, 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
24	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
25	TRIS	natural abundance	10 mM
26	Magnesium Chloride	natural abundance	0.5 mM
27	D2O	natural abundance	100 %

7 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
15	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
16	TRIS	natural abundance	10 mM
17	Magnesium Chloride	natural abundance	0.5 mM
18	D2O	natural abundance	100 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
24	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
25	TRIS	natural abundance	10 mM
26	Magnesium Chloride	natural abundance	0.5 mM
27	D2O	natural abundance	100 %

9 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
28	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri,Cyt,Gua	1 mM
29	TRIS	natural abundance	10 mM
30	Magnesium Chloride	natural abundance	0.5 mM
31	H2O	natural abundance	90 %
32	D2O	natural abundance	10 %

10 2D HNNOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
10	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
11	TRIS	natural abundance	10 mM
12	Magnesium Chloride	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

11 2D HNNOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
19	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
20	TRIS	natural abundance	10 mM
21	Magnesium Chloride	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

12 HNN-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
10	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
11	TRIS	natural abundance	10 mM
12	Magnesium Chloride	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

13 HNN-COSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
19	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
20	TRIS	natural abundance	10 mM
21	Magnesium Chloride	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

14 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
10	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Ade,Uri	1 mM
11	TRIS	natural abundance	10 mM
12	Magnesium Chloride	natural abundance	0.5 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

15 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.3

#	Name	Isotope labeling	Concentration
19	RNA_(48-MER)	[U-98% 13C; U-98% 15N]-Cyt,Gua	1 mM
20	TRIS	natural abundance	10 mM
21	Magnesium Chloride	natural abundance	0.5 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %

16 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Concentration
6	RNA_(48-MER)	natural abundance	1 mM
7	TRIS	natural abundance	10 mM
8	Magnesium Chloride	natural abundance	0.5 mM
9	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_19260_2m8k.nef
Input source #2: Coordindates	2m8k.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--------
GGUUUCUUUUUAGUGAUUUUUCCAAACCCCUUUGUGCAAAAAUCAUUA
||||||||||||||||||||||||||||||||||||||||||||||||
GGUUUCUUUUUAGUGAUUUUUCCAAACCCCUUUGUGCAAAAAUCAUUA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	48	0	0	100.0

Content subtype: combined_19260_2m8k.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	618		100.0 (chain: A, length: 48)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	939 (1)	noe	100.0 (chain: A, length: 48)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	89 (1)	hbond	83.3 (chain: A, length: 48)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	254 (254)	.	100.0 (chain: A, length: 48)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	98 (98)	.	97.9 (chain: A, length: 48)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 100.0%

--------10--------20--------30--------40--------
GGUUUCUUUUUAGUGAUUUUUCCAAACCCCUUUGUGCAAAAAUCAUUA
||||||||||||||||||||||||||||||||||||||||||||||||
GGUUUCUUUUUAGUGAUUUUUCCAAACCCCUUUGUGCAAAAAUCAUUA

Total number of assignments
- ¹H chemical shifts: 339
- ¹³C chemical shifts: 247
- ¹⁵N chemical shifts: 32

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	G	H21	6.292
2	G	H22	5.676
13	G	H21	6.491
15	G	H21	5.929
15	G	H22	5.807
16	A	H61	6.355
16	A	N1	221.7
24	A	H61	7.342
24	A	H62	6.146
24	A	N1	222.2
25	A	H61	8.125
25	A	H62	6.631
25	A	N1	221.1
26	A	H61	6.199
26	A	N1	220.4
34	G	H21	7.337
34	G	H22	5.658
36	G	H21	8.221
36	G	H22	6.606
38	A	H61	8.134
38	A	H62	7.525
38	A	N1	219.7
38	A	N7	227.2
39	A	H61	7.873
39	A	H62	7.596
39	A	N1	220.7
39	A	N7	227.3
40	A	H61	8.098
40	A	H62	7.6
40	A	N1	220.3
40	A	N7	224.9
41	A	H61	8.385
41	A	H62	7.373
41	A	N1	221.7
41	A	N7	225.5
42	A	H61	8.32
42	A	H62	7.87
42	A	N1	220.7
42	A	N7	227.1
45	A	H61	7.895
45	A	H62	7.518
45	A	N1	219.4

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	423	312	73.8
¹³C chemical shifts	330	247	74.8
¹⁵N chemical shifts	27	17	63.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	288	190	66.0
¹³C chemical shifts	240	162	67.5

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	135	122	90.4
¹³C chemical shifts	90	85	94.4
¹⁵N chemical shifts	27	17	63.0

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	30	29	96.7
¹³C chemical shifts	30	29	96.7

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 48, Sequence coverage: 100.0%
- Total number of restraints: 939
- Weight of restraints: 1.0 (939)
- Potential type of restraints: square-well-parabolic (939)
- Range of distance target values: 2.5, 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: 48, Sequence coverage: 83.3%
  - Total number of restraints: 89
  - Weight of restraints: 1.0 (89)
  - Potential type of restraints: square-well-parabolic (89)
  - Range of distance target values: 2.0, 2.9 (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: 48, Sequence coverage: 100.0%
- Total number of restraints: 254
- Total number of restraints per polymer type: 254
- Weight of restraints: 1.0 (254)
- Potential type of restraints: square-well-parabolic (254)
- 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: 48, Sequence coverage: 97.9%
- Total number of restraints: 98
- Potential type of restraints: square-well-parabolic (98)
- Range of observed RDC values: -88.14, 52.06 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords kluyveromyces lactis, nucleic acid, pseudoknot, RNA triplex, telomerase

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.351 seconds)

BMRB: 19260

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Sample #6

Sample #7

Related entities 1. RNA (48-MER), : 1 entities Detail

Experiments performed 16 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail