Summary information and primary citation
- PDB-id
-
2ixy;
DSSR-derived features in text and
JSON formats
- Class
- RNA
- Method
- NMR
- Summary
- Solution structure of the apical stem-loop of the human
hepatitis b virus encapsidation signal
- Reference
-
Flodell S, Petersen M, Girard F, Zdunek J, Kidd-Ljunggren
K, Schleucher J, Wijmenga S (2006): "Solution
structure of the apical stem-loop of the human hepatitis
B virus encapsidation signal." Nucleic Acids
Res., 34, 4449-4457. doi: 10.1093/nar/gkl582.
- 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.
