View source for 2ixy


==Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal==
<StructureSection load='2ixy' size='340' side='right'caption='[[2ixy]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ixy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepatitis_B_virus Hepatitis B virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IXY FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ixy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ixy OCA], [https://pdbe.org/2ixy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ixy RCSB], [https://www.ebi.ac.uk/pdbsum/2ixy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ixy ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.

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 Nucleic Acids Res. 2006;34(16):4449-57. Epub 2006 Aug 31. PMID:16945960<ref>PMID:16945960</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ixy" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Hepatitis B virus]]
[[Category: Large Structures]]
[[Category: Flodell S]]
[[Category: Girard F]]
[[Category: Kidd-Ljunggren K]]
[[Category: Petersen M]]
[[Category: Schleucher J]]
[[Category: Wijmenga SS]]
[[Category: Zdunek J]]