BMRB Entry 15157

Name: NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus
Published: 2007-06-06

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PDB ID: 2oj7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15157
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus

Deposition date:

2007-03-08

Original release date:

2007-06-06

Authors:

Girard, F.; Ottink, O.; Ampt, K.; Tessari, M.; Wijmenga, S.

Citation:

Citation: Girard, F.; Ottink, O.; Ampt, K.; Tessari, M.; Wijmenga, S.. "Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals" Nucleic Acids Res. 35, 2800-2811 (2007).
PubMed: 17430968

Assembly members:

Assembly members:
GCUGUUGU, polymer, 8 residues, Formula weight is not available

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GCUGUUGU: GCUGUUGU

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
15N chemical shifts	2
1H chemical shifts	27

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA	1

Entities:

Entity 1, RNA 8 residues - Formula weight is not available

1

G

C

U

G

U

G

U

Samples:

sample_1: 5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3' 1.2 mM; sodium phosphate 10 mM; EDTA 0.1 mM; H2O 95%; D2O 5%

sample_2: 5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3', [U-13C; U-15N; U-2H], 1 mM; sodium phosphate 10 mM; EDTA 0.1 mM; H2O 95%; D2O 5%

sample_3: 5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3' 1.2 mM; sodium phosphate 10 mM; EDTA 0.1 mM; D2O 100%

sample_4: 5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3', [U-13C; U-15N; U-2H], 1.0 mM; sodium phosphate 10 mM; EDTA 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 10 mM; pH: 6.7; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 6.7; pressure: 1 atm; temperature: 288 K

sample_conditions_3: ionic strength: 10 mM; pH: 6.7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_2
HMQC-15N/1H	sample_2	isotropic	sample_conditions_1
DQF-COSY	sample_3	isotropic	sample_conditions_3
HMQC-13C/1H	sample_4	isotropic	sample_conditions_3
2D NOESY	sample_3	isotropic	sample_conditions_3

Software:

X-PLOR v3.851*, Brunger - refinement

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 800 MHz