BMRB Entry 15656

Name: Apical Stem Loop Duck HBV
Published: 2008-09-12

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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:

Apical Stem Loop Duck HBV

Deposition date:

2008-02-13

Original release date:

2008-09-12

Authors:

Ampt, Kirsten; Ottink, Otmar; Girard, Fred; Nelissen, Frank; Tessari, Marco; Wijmenga, Sybren

Citation:

Citation: Ampt, Kirsten; Ottink, Otmar; Girard, Fred; Nelissen, Frank; Tessari, Marco; Wijmenga, Sybren. "1H, 13C and 15N NMR assignments of Duck HBV apical stem loop of the epsilon encapsidation signal" Biomol. NMR Assignments 2, 159-162 (2008).
PubMed: 19636894

Assembly members:

Assembly members:
Duck_HBV_apical_loop, polymer, 29 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Hepatitis B virus Taxonomy ID: 10407 Superkingdom: Viruses Kingdom: not available Genus/species: Orthohepadnavirus Hepatitis B virus

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Duck_HBV_apical_loop: GGUCUACAUUGCUGUUGUCG UGUGUGACC

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	194
15N chemical shifts	45
1H chemical shifts	315

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	APIC	1

Entities:

Entity 1, APIC 29 residues - Formula weight is not available

1

G

U

C

U

A

C

A

U

2

G

C

U

G

U

G

U

C

G

3

U

G

U

G

U

G

A

C

Samples:

sample_1: Duck HBV apical loop 1.2 mM; sodium phosphate buffer 10 mM; EDTA 0.1 mM; H2O 95%; D2O 5%

sample_2: Duck HBV apical loop 1.2 mM; sodium phosphate buffer 10 mM; EDTA 0.1 mM; D2O 100%

sample_3: Duck HBV apical loop, [U-13C; U-15N]-Ura, 1 mM; sodium phosphate buffer 10 mM; EDTA 0.1 mM; D2O 5%; H2O 95%

sample_4: Duck HBV apical loop, [U-13C; U-15N]-Ura, 1 mM; sodium phosphate buffer 10 mM; EDTA 0.1 mM; D2O 100%

sample_5: Duck HBV apical loop, [U-13C; U-15N], 0.7 mM; sodium phosphate buffer 10 mM; EDTA 0.1 mM; D2O 5%; H2O 95%; DSS 1 mM

sample_6: Duck HBV apical loop, [U-13C; U-15N], 0.7 mM; sodium phosphate buffer 10 mM; EDTA 0.1 mM; D2O 5%; H2O 95%; Pf1 phage 15 mg/ml

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 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_3
3D 1H-13C NOESY	sample_5	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_3
2D 1H-1H COSY	sample_5	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_5	isotropic	sample_conditions_2
3D HCN	sample_5	isotropic	sample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment, peak picking

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Varian INOVA 800 MHz