BMRB Entry 30701

Name: 61 nt human Hepatitis B virus epsilon pre-genomic RNA
Published: 2020-12-26

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PDB ID: 6var
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30701
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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: 61 nt human Hepatitis B virus epsilon pre-genomic RNA PubMed: 34155954

Deposition date: 2019-12-17 Original release date: 2020-12-26

Authors: LeBlanc, R.; Kasprzak, W.; Longhini, A.; Abulwerdi, F.; Ginocchio, S.; Shields, B.; Nyman, J.; Svirydava, M.; Del Vecchio, C.; Ivanic, J.; Schneekloth, J.; Dayie, T.; Shapiro, B.; Le Grice, S.

Citation: LeBlanc, Regan; Kasprzak, Wojciech; Longhini, Andrew; Olenginski, Lukasz; Abulwerdi, Fardokht; Ginocchio, Stefano; Shields, Brigit; Nyman, Julie; Svirydava, Maryia; Del Vecchio, Claudia; Ivanic, Joseph; Schneekloth, John; Shapiro, Bruce; Dayie, Theodore Kwaku; Le Grice, Stuart. "Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA" J. Biomol. Struct. Dyn. 40, 9761-9773 (2022).

Assembly members:
entity_1, polymer, 61 residues, 19541.488 Da.

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

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: GGUUCAUGUCCUACUGUUCA AGCCUCCAAGCUGUGCCUUG GGUGGCUUUGGGGCAUGGAC C

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	164
15N chemical shifts	27
1H chemical shifts	283

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 61 residues - 19541.488 Da.

1

G

U

C

A

U

G

U

C

2

C

U

A

C

U

G

U

C

A

3

A

G

C

U

C

A

G

4

C

U

G

U

G

C

U

G

5

G

U

G

C

U

G

6

G

C

A

U

G

A

C

7

C

Samples:

sample_1: RNA (61-MER), [U-13C; U-15N], 0.8 mM

sample_2: RNA (61-MER), [U-13C; U-15N], 0.8 mM

sample_3: RNA (61-MER), 13C-selective, 0.7 mM

sample_conditions_1: ionic strength: 10 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
3D HCN	sample_1	isotropic	sample_conditions_1
2D HNCCNCH	sample_2	isotropic	sample_conditions_1
Filter/Edit NOESY	sample_3	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMRView, Johnson, One Moon Scientific - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Ascend 800 MHz
Bruker Ultrashield Plus 600 MHz