BMRBj - BMREntryMaster

Found 1 Document (0.346 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

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 (0.346 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

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 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