2IXY

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

Summary for 2IXY

• Entry DOI: 10.2210/pdb2ixy/pdb
• Related: 2IXZ
• Descriptor: 5'-R(*GP*GP*CP*CP*UP*CP*CP*AP*AP*GP *CP*UP*GP*UP*GP*CP*CP*UP*UP*GP*GP*GP*UP*GP*GP*CP*C)-3' (1 entity in total)
• Functional Keywords: hbv, rdc, rna, pseudo triloop
• Biological source: HEPATITIS B VIRUS
• Total number of polymer chains: 1
• Total formula weight: 8649.15

Authors

Flodell, S.,Petersen, M.,Girard, F.,Zdunek, J.,Kidd-Ljunggren, K.,Schleucher, J.,Wijmenga, S.S. (deposition date: 2006-07-11, release date: 2006-09-06, Last modification date: 2024-05-15)

Primary citation

Flodell, S.,Petersen, M.,Girard, F.,Zdunek, J.,Kidd-Ljunggren, K.,Schleucher, J.,Wijmenga, S.
Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal.
Nucleic Acids Res., 34:4449-4457, 2006

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.

PubMed: 16945960
DOI: 10.1093/nar/gkl582

Experimental method

SOLUTION NMR