BMRB Entry 15745

Name: Solution structure of stem-loop alpha; of the hepatitis B virus post-transcriptional regulatory element
Published: 2008-09-25

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PDB ID: 2jym
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15745
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2008-04-28

Original release date:

2008-09-25

Authors:

Ohlenschlager, Oliver; Gorlach, Matthias; Schwalbe, Martin

Citation:

Citation: Schwalbe, Martin; Ohlenschlager, Oliver; Marchanka, Aliaksandr; Ramachandran, Ramadurai; Hafner, Sabine; Heise, Tilman; Gorlach, Matthias. "Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element" Nucleic Acids Research 36, 1681-1689 (2008).
PubMed: 18263618

Assembly members:

Assembly members:
RNA, polymer, 22 residues, 7105.313 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pUC19

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RNA: GGCUCGCAGCAGGUCUGGAG UC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	145
15N chemical shifts	50
1H chemical shifts	195

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RNA (5'-R(GPGPCPUPCPGPCPAPGPCPAPGPGPUPCPUPGPGPAPGPUPC)-3')	1

Entities:

Entity 1, RNA (5'-R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP*GP*UP*C)-3') 22 residues - 7105.313 Da.

1

G

C

U

C

G

C

A

G

C

2

A

G

U

C

U

G

A

G

3

U

C

Samples:

sample_1: RNA (5'-R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP*GP*UP*C)-3'), [U-100% 13C; U-100% 15N], 1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 0.2 mM; D2O 10%; H2O 90%

sample_2: RNA (5'-R(*GP*GP*CP*UP*CP*GP*CP*AP*GP*CP*AP*GP*GP*UP*CP*UP*GP*GP*AP*GP*UP*C)-3'), [U-100% 13C; U-100% 15N], 1 mM; potassium phosphate 10 mM; potassium chloride 40 mM; EDTA 0.2 mM; D2O 99%

sample_conditions_1: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.2; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2

Software:

CYANA v2.0, Guntert, Mumenthaler and Wuthrich - structure solution

XEASY, Bartels et al. - chemical shift assignment, peak picking

VNMR, Varian - collection, processing

OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - collection, refinement

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz