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Found 1 Document (0.413 seconds)

BMRB: 15745

2JYM

Solution structure of stem-loop alpha; of the hepatitis B virus post-transcriptional regulatory element

Authors

Ohlenschlager, O., Gorlach, M., Schwalbe, M.

Assembly

HBV stem-loop alpha;

Entity

1. HBV stem-loop alpha; (polymer, Thiol state: not present), 22 monomers, 7168.237 Da Detail

GGCUCGCAGC AGGUCUGGAG UC

Formula weight

7168.237 Da

Source organism

Hepatitis B virus

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.3 %, Completeness (bb): 100.0 % Detail

Polymer type: polyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	98.3 % (344 of 350)	98.4 % (189 of 192)	100.0 % (145 of 145)	76.9 % (10 of 13)
Suger, PO4	100.0 % (242 of 242)	100.0 % (132 of 132)	100.0 % (110 of 110)
Nucleobase	94.4 % (102 of 108)	95.0 % (57 of 60)	100.0 % (35 of 35)	76.9 % (10 of 13)
Aromatic	93.8 % (90 of 96)	93.8 % (45 of 48)	100.0 % (35 of 35)	76.9 % (10 of 13)

1. RNA

GGCUCGCAGC AGGUCUGGAG UC

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
2	potassium phosphate	natural abundance	10 mM
3	potassium chloride	natural abundance	40 mM
4	EDTA	natural abundance	0.2 mM
5	D2O		10 %
6	H2O	natural abundance	90 %

Sample #2

Solvent system 99% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
8	potassium phosphate	natural abundance	10 mM
9	potassium chloride	natural abundance	40 mM
10	EDTA	natural abundance	0.2 mM
11	D2O		99 %

Release date

2008-09-24

Citation

Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element
Schwalbe, M., Ohlenschlager, O., Marchanka, A., Ramachandran, R., Hafner, S., Heise, T., Gorlach, M.
Nucleic Acids Res. (2008), 36, 1681-1689, PubMed 18263618 , DOI 10.1093/nar/gkn006 , Abstract

Related entities 1. HBV stem-loop alpha;, : 1 entities Detail

Experiments performed 6 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 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
2	potassium phosphate	natural abundance	10 mM
3	potassium chloride	natural abundance	40 mM
4	EDTA	natural abundance	0.2 mM
5	D2O		10 %
6	H2O	natural abundance	90 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
2	potassium phosphate	natural abundance	10 mM
3	potassium chloride	natural abundance	40 mM
4	EDTA	natural abundance	0.2 mM
5	D2O		10 %
6	H2O	natural abundance	90 %

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 99% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
8	potassium phosphate	natural abundance	10 mM
9	potassium chloride	natural abundance	40 mM
10	EDTA	natural abundance	0.2 mM
11	D2O		99 %

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
2	potassium phosphate	natural abundance	10 mM
3	potassium chloride	natural abundance	40 mM
4	EDTA	natural abundance	0.2 mM
5	D2O		10 %
6	H2O	natural abundance	90 %

5 3D 1H-13C NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 99% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
8	potassium phosphate	natural abundance	10 mM
9	potassium chloride	natural abundance	40 mM
10	EDTA	natural abundance	0.2 mM
11	D2O		99 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 99% D2O, Pressure 1 atm, Temperature 293 K, pH 6.2

#	Name	Isotope labeling	Concentration
7	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	[U-100% 13C; U-100% 15N]	1 mM
8	potassium phosphate	natural abundance	10 mM
9	potassium chloride	natural abundance	40 mM
10	EDTA	natural abundance	0.2 mM
11	D2O		99 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15745_2jym.nef
Input source #2: Coordindates	2jym.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--
GGCUCGCAGCAGGUCUGGAGUC
||||||||||||||||||||||
GGCUCGCAGCAGGUCUGGAGUC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	22	0	0	100.0

Content subtype: combined_15745_2jym.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	390		100.0 (chain: A, length: 22)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	675 (1)	noe	100.0 (chain: A, length: 22)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	206 (205)	.	100.0 (chain: A, length: 22)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: OK
Sequence coverage of experimental data
- Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 195
- ¹³C chemical shifts: 145
- ¹⁵N chemical shifts: 50

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	G	N9	170.36
2	G	H21	6.28
2	G	H22	6.28
2	G	N2	74.54
2	G	N9	171.74
3	C	N1	153.08
3	C	N3	198.72
3	C	N4	100.91
4	U	N1	147.81
5	C	N1	152.29
5	C	N3	198.38
5	C	N4	99.91
6	G	N9	169.17
7	C	N1	150.68
7	C	N4	97.12
8	A	H62	7.27
8	A	H61	6.92
8	A	N1	221.44
8	A	N6	83.05
8	A	N9	171.13
9	G	N9	170.9
10	C	N1	149.11
10	C	N3	195.9
10	C	N4	100.38
11	A	N9	168.97
12	G	N9	170.03
13	G	N9	170.14
14	U	N1	145.8
15	C	N1	150.98
15	C	N3	199.1
15	C	N4	97.63
16	U	N1	147.75
17	G	N9	170.97
18	G	N2	76.08
18	G	N9	170.48
19	A	H62	7.71
19	A	H61	7.38
19	A	N1	222.42
19	A	N6	84.4
19	A	N9	172.54
20	G	N2	76.14
20	G	N9	171.0
21	U	N1	147.11
22	C	N1	152.37
22	C	N3	198.01
22	C	N4	100.36

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	192	189	98.4
¹³C chemical shifts	145	145	100.0
¹⁵N chemical shifts	13	10	76.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	132	132	100.0
¹³C chemical shifts	110	110	100.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	57	95.0
¹³C chemical shifts	35	35	100.0
¹⁵N chemical shifts	13	10	76.9

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	15	15	100.0
¹³C chemical shifts	15	15	100.0

Histogram of normalized assigned chemical shifts

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
- Total number of restraints: 675
- Weight of restraints: 1.0 (675)
- Potential type of restraints: upper-bound-parabolic (675)
- Range of distance target values: 1.8, 6.97 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 22, Sequence coverage: 100.0%
- Total number of restraints: 205
- Total number of restraints per polymer type: 205
- Weight of restraints: 1.0 (205)
- Potential type of restraints: square-well-parabolic (205)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords hepatitis B virus, NMR solution structure, post-transcriptional regulatory element, stem-loop alpha;

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Found 1 Document (0.413 seconds)

BMRB: 15745

Sample #1

Sample #2

Related entities 1. HBV stem-loop alpha;, : 1 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail