2IXZ

Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 12 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal.

Flodell, S.Petersen, M.Girard, F.Zdunek, J.Kidd-Ljunggren, K.Schleucher, J.Wijmenga, S.

(2006) Nucleic Acids Res 34: 4449-4457

  • DOI: https://doi.org/10.1093/nar/gkl582
  • Primary Citation of Related Structures:  
    2IXY, 2IXZ

  • PubMed Abstract: 

    Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the apical stem-loop based on NOE, RDC and (1)H chemical shift NMR data. The (1)H chemical shifts proved to be crucial to define the loop conformation. The loop sequence 5'-CUGUGC-3' folds into a UGU triloop with a CG closing base pair and a bulged out C and hence forms a pseudo-triloop, a proposed protein recognition motif. In the UGU loop conformations most consistent with experimental data, the guanine nucleobase is located on the minor groove face and the two uracil bases on the major groove face. The underlying helix is disrupted by a conserved non-paired U bulge. This U bulge adopts multiple conformations, with the nucleobase being located either in the major groove or partially intercalated in the helix from the minor groove side, and bends the helical stem. The pseudo-triloop motif, together with the U bulge, may represent important anchor points for the initial recognition of epsilon by the viral RT.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*GP*CP*UP*GP*UP*GP*CP*CP)-3'8Hepatitis B virus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 12 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references, Other