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- PDB-6var: 61 nt human Hepatitis B virus epsilon pre-genomic RNA -

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Basic information

Entry
Database: PDB / ID: 6var
Title61 nt human Hepatitis B virus epsilon pre-genomic RNA
ComponentsRNA (61-MER)
KeywordsRNA / non-coding RNA / viral RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHepatitis B virus
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsLeBlanc, R.M. / Kasprzak, W.K. / Longhini, A.P. / Abulwerdi, F. / Ginocchio, S. / Shields, B. / Nyman, J. / Svirydava, M. / Del Vecchio, C. / Ivanic, J. ...LeBlanc, R.M. / Kasprzak, W.K. / Longhini, A.P. / Abulwerdi, F. / Ginocchio, S. / Shields, B. / Nyman, J. / Svirydava, M. / Del Vecchio, C. / Ivanic, J. / Schneekloth, J.S. / Dayie, T.K. / Shapiro, B.A. / Le Grice, S.F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2021
Title: Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA.
Authors: LeBlanc, R.M. / Kasprzak, W.K. / Longhini, A.P. / Olenginski, L.T. / Abulwerdi, F. / Ginocchio, S. / Shields, B. / Nyman, J. / Svirydava, M. / Del Vecchio, C. / Ivanic, J. / Schneekloth Jr., ...Authors: LeBlanc, R.M. / Kasprzak, W.K. / Longhini, A.P. / Olenginski, L.T. / Abulwerdi, F. / Ginocchio, S. / Shields, B. / Nyman, J. / Svirydava, M. / Del Vecchio, C. / Ivanic, J. / Schneekloth Jr., J.S. / Shapiro, B.A. / Dayie, T.K. / Le Grice, S.F.J.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 4, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Aug 25, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (61-MER)


Theoretical massNumber of molelcules
Total (without water)19,5411
Polymers19,5411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (61-MER)


Mass: 19541.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepatitis B virus

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
142isotropic13D 1H-15N NOESY
151isotropic13D 1H-13C NOESY aliphatic
161isotropic13D 1H-13C NOESY aromatic
172isotropic22D 1H-1H NOESY
181isotropic22D 1H-1H NOESY
191isotropic13D HCN
1102isotropic12D HNCCNCH
1113isotropic1Filter/Edit NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.8 mM [U-13C; U-15N] RNA (61-MER), 100% D2O13C/15N_D2O100% D2O
solution20.8 mM [U-13C; U-15N] RNA (61-MER), 90% H2O/10% D2O13C/15N_H2O90% H2O/10% D2O
solution30.7 mM 13C-selective RNA (61-MER), 100% D2Oselective-UGC-C1'-A-C2'100% D2OThis sample was made from 13C-C1',C6/6-UGC and 13C-C2',C8-A rNTPs made in-house
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMRNA (61-MER)[U-13C; U-15N]1
0.8 mMRNA (61-MER)[U-13C; U-15N]2
0.7 mMRNA (61-MER)13C-selective3
Sample conditionsDetails: sodium phosphate buffer / Ionic strength: 10 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AscendBrukerAscend8001
Bruker Ultrashield PlusBrukerUltrashield Plus6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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