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Found 1 Document (0.373 seconds)

BMRB: 15417

2JTP

Solution Structure of the Frameshift-Inducing RNA Stem-Loop in SIV

Authors

Marcheschi, R.J., Staple, D.W., Butcher, S.E.

Assembly

34mer RNA

Entity

1. 34mer RNA (polymer, Thiol state: not present), 34 monomers, 10975.55 Da Detail

GGAUGGGGAA AGAAGCCCCG CAAUUUCCCC AUCC

Formula weight

10975.55 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 67.5 %, Completeness (bb): 58.3 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	67.5 % (366 of 542)	74.6 % (223 of 299)	59.8 % (137 of 229)	42.9 % (6 of 14)
Suger, PO4	58.3 % (218 of 374)	67.2 % (137 of 204)	47.6 % (81 of 170)
Nucleobase	88.1 % (148 of 168)	90.5 % (86 of 95)	94.9 % (56 of 59)	42.9 % (6 of 14)
Aromatic	91.8 % (134 of 146)	98.6 % (72 of 73)	94.9 % (56 of 59)	42.9 % (6 of 14)

1. SIV RNA (34-MER)

GGAUGGGGAA AGAAGCCCCG CAAUUUCCCC AUCC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SIV17-50 RNA (34-MER)	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O		10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	SIV17-50 RNA (34-MER)	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O		10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
10	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

Release date

2007-09-17

Citation

Programmed ribosomal frameshifting in SIV is induced by a highly structured RNA stem-loop
Marcheschi, R.J., Staple, D.W., Butcher, S.E.
J. Mol. Biol. (2007), 373, 652-663, PubMed 17868691 , DOI 10.1016/j.jmb.2007.08.033 , Abstract

Related entities 1. 34mer RNA, : 1 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	SIV17-50 RNA (34-MER)	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

2 2D 1H-1H NOESY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
4	SIV17-50 RNA (34-MER)	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O		10 %

3 2D 1H-1H COSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SIV17-50 RNA (34-MER)	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O		10 %

4 2D 1H-15N HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
10	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

5 2D 1H-13C HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
10	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

6 3D 1H-13C-1H HCCH-TOCSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
10	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

7 3D NOESY-HMQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
10	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
11	H2O	natural abundance	90 %
12	D2O		10 %

8 J-MODULATED 1H-13C CT-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O		10 %

9 J-MODULATED 1H-13C CT-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	SIV17-50 RNA (34-MER)	[U-100% 13C; U-100% 15N]	1 mM
8	H2O	natural abundance	90 %
9	D2O		10 %

10 2D 1H-1H NOESY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 277 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SIV17-50 RNA (34-MER)	natural abundance	1 mM
2	H2O	natural abundance	90 %
3	D2O		10 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_15417_2jtp.nef
Input source #2: Coordindates	2jtp.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----
GGAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUCC
||||||||||||||||||||||||||||||||||
GGAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUCC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	34	0	0	100.0

Content subtype: combined_15417_2jtp.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	397		100.0 (chain: A, length: 34)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	667 (1)	noe	100.0 (chain: A, length: 34)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	36 (1)	undefined	79.4 (chain: A, length: 34)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	72 (1)	hbond	82.4 (chain: A, length: 34)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	219 (219)	.	100.0 (chain: A, length: 34)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_7	OK	28 (28)	.	64.7 (chain: A, length: 34)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: OK

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%

--------10--------20--------30----
GGAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUCC
||||||||||||||||||||||||||||||||||
GGAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUCC

Total number of assignments
- ¹H chemical shifts: 249
- ¹³C chemical shifts: 137
- ¹⁵N chemical shifts: 11

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	5.728
2	G	H22	6.718
3	A	H61	6.401
3	A	H62	7.801
5	G	H21	5.597
5	G	H22	6.699
6	G	H21	5.646
6	G	H22	6.682
7	G	H21	5.678
7	G	H22	6.69
8	G	H21	5.645
8	G	H22	6.705
9	A	H61	6.407
9	A	H62	7.574
10	A	H61	6.466
10	A	H62	7.567
11	A	H61	6.257
11	A	H62	6.802
12	G	H21	7.584
12	G	H22	6.256
15	G	H21	5.49
15	G	H22	6.814
20	G	H21	5.469
20	G	H22	6.327
27	C	N3	197.473
28	C	N3	196.457
29	C	N3	196.422
30	C	N3	195.67
31	A	H61	6.279
31	A	H62	7.592
33	C	N3	197.597

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	299	223	74.6
¹³C chemical shifts	229	137	59.8
¹⁵N chemical shifts	14	6	42.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	204	137	67.2
¹³C chemical shifts	170	81	47.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	95	86	90.5
¹³C chemical shifts	59	56	94.9
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	27	27	100.0
¹³C chemical shifts	27	27	100.0

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: 34, Sequence coverage: 100.0%
- Total number of restraints: 667
- Weight of restraints: 1.0 (667)
- Potential type of restraints: square-well-parabolic (667)
- Range of distance target values: 2.15, 5.5 (Å)
- Histogram of 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: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 79.4%
  - Total number of restraints: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: square-well-parabolic (36)
  - Range of distance target values: 5.6, 18.0 (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: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 82.4%
    - Total number of restraints: 72
    - Weight of restraints: 1.0 (72)
    - Potential type of restraints: square-well-parabolic (72)
    - 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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 100.0%
- Total number of restraints: 219
- Total number of restraints per polymer type: 219
- Weight of restraints: 1.0 (219)
- Potential type of restraints: square-well-parabolic (219)
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 34, Sequence coverage: 64.7%
- Total number of restraints: 28
- Potential type of restraints: square-well-parabolic (28)
- Range of observed RDC values: -46.61, 51.97 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None

Keywords Frameshifting, HIV-2, RNA Stem-Loop, SIV, Triloop

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Found 1 Document (0.373 seconds)

BMRB: 15417

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. 34mer RNA, : 1 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 7 contents Detail