6VAR | pdb_00006var

61 nt human Hepatitis B virus epsilon pre-genomic RNA

• PDB DOI: https://doi.org/10.2210/pdb6VAR/pdb
• BMRB: 30701
• NAKB: 6VAR

• Classification: RNA
• Organism(s): Hepatitis B virus
• Mutation(s): No 


• Deposited: 2019-12-17 Released: 2020-12-30 
• Deposition Author(s): 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 Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

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• Method: SOLUTION SCATTERING

Literature

Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA.

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.

(2021) J Biomol Struct Dyn : 1-13

• PubMed: 34155954 
• DOI: https://doi.org/10.1080/07391102.2021.1934544
• Primary Citation Related Structures: 
  6VAR


• PubMed Abstract: 
  

  Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral polymerase with a cis -acting regulatory signal, designated epsilon (ε), located at the 5'-end of its pre-genomic RNA (pgRNA). Binding of polymerase to ε is also necessary for pgRNA encapsidation. While the mechanistic basis of this interaction remains elusive, mutagenesis studies suggest its internal 6-nt "priming loop" provides an important structural contribution. ε might therefore be considered a promising target for small molecule interventions to complement current nucleoside-analog based anti-HBV therapies. An ideal prerequisite to any RNA-directed small molecule strategy would be a detailed structural description of this important element. Herein, we present a solution NMR structure for HBV ε which, in combination with molecular dynamics and docking simulations, reports on a flexible ligand "pocket", reminiscent of those observed in proteins. We also demonstrate the binding of the selective estrogen receptor modulators (SERMs) Raloxifene, Bazedoxifene, and a de novo derivative to the priming loop.Communicated by Ramaswamy H. Sarma.

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Organizational Affiliation: 
• Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA.
Vertex Pharmaceuticals, Boston, MA, USA.
Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA.
Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA.
Department of Molecular Medicine, University of Padua, Padua, Italy.
Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 19.54 kDa 
• Atom Count: 1,290 
• Modeled Residue Count: 61 
• Deposited Residue Count: 61 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (61-MER)	A	61	Hepatitis B virus

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

• Method: SOLUTION SCATTERING

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2021-08-04
  Changes: Database references
• Version 1.3: 2021-08-11
  Changes: Database references
• Version 1.4: 2021-08-25
  Changes: Database references
• Version 1.5: 2023-06-14
  Changes: Other
• Version 1.6: 2024-05-15
  Changes: Data collection, Database references