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Found 1 Document (0.429 seconds)

BMRB: 17406

2L8F

Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon

Authors

Lerman, Y.V., Kennedy, S.D., Turner, D.H.

Assembly

5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'

Entity

1. RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3') (polymer), 11 monomers, 3585.126 Da Detail

GUGAAGCCCG U

2. RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3') (polymer), 11 monomers, 3608.166 Da Detail

CGGAGGACAC U

Total weight

7193.292 Da

Max. entity weight

3608.166 Da

Source organism

Bombyx mori

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 52.4 %, Completeness (bb): 40.5 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N	³¹P
All	52.4 % (194 of 370)	74.3 % (142 of 191)	16.4 % (24 of 146)	72.7 % (8 of 11)	90.9 % (20 of 22)
Suger, PO4	40.5 % (107 of 264)	65.9 % (87 of 132)	0.0 % (0 of 110)		90.9 % (20 of 22)
Nucleobase	82.1 % (87 of 106)	93.2 % (55 of 59)	66.7 % (24 of 36)	72.7 % (8 of 11)
Aromatic	81.9 % (77 of 94)	95.7 % (45 of 47)	66.7 % (24 of 36)	72.7 % (8 of 11)

1. RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3')

GUGAAGCCCG U

2. RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')

CGGAGGACAC U

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

Release date

2011-08-16

Citation

NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions
Lerman, Y.V., Kennedy, S.D., Shankar, N., Parisien, M., Major, F., Turner, D.H.
RNA (2011), 17, 1664-1677, PubMed 21778280 , DOI 10.1261/rna.2641911 , Abstract

Related entities 1. RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3'), : 1 entities Detail

Related entities 2. RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3'), : 1 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

5 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

7 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
2	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
3	sodium chloride	natural abundance	80 mM
4	sodium phosphate	natural abundance	10 mM
5	EDTA	natural abundance	0.5 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

9 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

10 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

11 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

12 2D 1H-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

13 2D 31P-1H COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3')	natural abundance	1.5 mM
9	RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3')	natural abundance	1.5 mM
10	sodium chloride	natural abundance	80 mM
11	sodium phosphate	natural abundance	10 mM
12	EDTA	natural abundance	0.5 mM
13	D2O	natural abundance	100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17406_2l8f.nef
Input source #2: Coordindates	2l8f.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-
GUGAAGCCCGU
|||||||||||
GUGAAGCCCGU

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

-------20--
CGGAGGACACU
|||||||||||
CGGAGGACACU
--------10-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	11	0	0	100.0
B	B	11	0	0	100.0

Content subtype: combined_17406_2l8f.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	208		100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)
1	Distance restraints	AMBER_distance_constraints_4	Warning	197 (1)	noe	100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)
2	Distance restraints	AMBER_distance_constraints_5	Warning	35 (1)	hbond	90.9 (chain: A, length: 11), 90.9 (chain: B, length: 11)
1	Dihedral angle restraints	AMBER_dihedral_3	OK	135 (135)	.	100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 156
- ¹³C chemical shifts: 24
- ¹⁵N chemical shifts: 8
- ³¹P chemical shifts: 20

Completeness of assignments

Entity_assemble_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	H22	8.632
1	G	H21	6.598
2	U	P	-1.222
3	G	H22	8.19
3	G	H21	6.175
3	G	P	-0.47
4	A	P	-0.754
5	A	P	-1.869
6	G	H21	6.581
6	G	H22	6.581
6	G	P	-1.259
7	C	P	-1.049
8	C	P	-0.969
9	C	P	-1.101
10	G	P	-0.75
11	U	P	-0.911

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	96	72	75.0
¹³C chemical shifts	73	10	13.7
¹⁵N chemical shifts	6	3	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	44	66.7
¹³C chemical shifts	55	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	28	93.3
¹³C chemical shifts	18	10	55.6
¹⁵N chemical shifts	6	3	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	8	100.0
¹³C chemical shifts	8	7	87.5

Entity_assemble_ID: B

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
13	G	H22	8.05
13	G	H21	6.021
13	G	P	-0.63
14	G	P	-1.271
15	A	P	-1.272
16	G	H21	6.223
16	G	H22	6.223
16	G	P	-1.0
17	G	H22	9.38
17	G	H21	5.436
17	G	P	-1.768
18	A	P	2.426
19	C	P	-1.375
20	A	H62	8.116
20	A	H61	6.478
20	A	P	-1.041
21	C	P	-1.001
22	U	P	-0.83

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	70	73.7
¹³C chemical shifts	73	14	19.2
¹⁵N chemical shifts	5	5	100.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	43	65.2
¹³C chemical shifts	55	0	0.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	27	93.1
¹³C chemical shifts	18	14	77.8
¹⁵N chemical shifts	5	5	100.0

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	10	10	100.0
¹³C chemical shifts	10	10	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: AMBER_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 197
- Weight of restraints: 1.0 (197)
- Potential type of restraints: square-well-parabolic (197)
- Range of distance target values: 2.65, 10.25 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: AMBER_distance_constraints_5
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 90.9%
    - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 90.9%
  - Total number of restraints: 35
  - Weight of restraints: 1.0 (35)
  - Potential type of restraints: square-well-parabolic (35)
  - Range of distance target values: 2.35, 7.25 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 135
- Total number of restraints per polymer type: 135
- Weight of restraints: 1.0 (135)
- Potential type of restraints: square-well-parabolic (135)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords 3RRs, internal loop, retrotransposon, RNA motif

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Found 1 Document (0.429 seconds)

BMRB: 17406

Sample #1

Sample #2

Related entities 1. RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), : 1 entities Detail

Related entities 2. RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), : 1 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail

Related entities 1. RNA (5'-R(GPUPGPAPAPGPCPCPCPGP*U)-3'), : 1 entities Detail

Related entities 2. RNA (5'-R(CPGPGPAPGPGPAPCPAPCP*U)-3'), : 1 entities Detail