2OJ8

NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus

Summary for 2OJ8

• Entry DOI: 10.2210/pdb2oj8/pdb
• Related: 2OJ7
• NMR Information: BMRB: 15157
• Descriptor: 5'-R(P*GP*CP*UP*GP*UP*UP*GP*U)-3' (1 entity in total)
• Functional Keywords: hbv, rna, epsilon, duck, uguu, tetraloop
• Total number of polymer chains: 1
• Total formula weight: 2520.51

Authors

Girard, F.C.,Ottink, O.M.,Ampt, K.A.M.,Tessari, M.,Wijmenga, S.S. (deposition date: 2007-01-12, release date: 2007-05-22, Last modification date: 2023-12-27)

Primary citation

Girard, F.C.,Ottink, O.M.,Ampt, K.A.,Tessari, M.,Wijmenga, S.S.
Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals.
Nucleic Acids Res., 35:2800-2811, 2007

PubMed Abstract: Hepatitis B virus (HBV) replication is initiated by binding of its reverse transcriptase (P) to the apical stem-loop (AL) and primer loop (PL) of epsilon, a highly conserved RNA element at the 5'-end of the RNA pregenome. Mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their P-epsilon interaction. Here, NMR and UV thermodynamic data on AL (and PL) from these three species are presented. The stabilities of the duck and heron ALs were found to be similar, and much lower than that of human. NMR data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron AL. In duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 35 degrees C well below the overall AL melting temperature. Surprisingly, the duck- and heron ALs were both found to be capped by a stable well-structured UGUU tetraloop. All avian ALs are expected to adhere to this because of their conserved sequence. Duck PL is stable and structured and, in view of sequence similarities, the same is expected for heron - and human PL.

PubMed: 17430968
DOI: 10.1093/nar/gkm131

Experimental method

SOLUTION NMR