This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2k5z

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 14:05, 10 September 2015

Solution structure and dynamics of the apical stem-loop of Duck hepatitis B virus

Structural highlights

2k5z is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2oj7, 2oj8, 2k5y
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Publication Abstract from PubMed

Hepatitis B virus (HBV) replication starts with binding of reverse transcriptase (RT) to the apical stem-loop region of epsilon, a conserved element of the RNA pregenome. For duck HBV, an in vitro replication system has provided molecular details of this interaction. Further insights can be obtained from the structure and dynamics of the duck and human apical stem-loops. Previously, we reported these for the human apical stem-loop. Here, we present the same for the duck counterpart. Unlike its human counterpart, the duck apical stem is unstable in its middle/upper part and contains noncanonical base pairs. This dynamics study is the first of an unstable RNA-DNA stem. Similar to the human stem, the duck apical stem comprises two helical segments with a bend angle of ca. 10 degrees , separated by a nonpaired mobile U residue. It is capped by a well-structured conserved UGUU loop with two residues mobile on the pico- to nanosecond time scale, one of which is involved in RT binding. Remarkably, the unstable middle/upper part of the stem does not show enhanced pico- to nanosecond time scale dynamics. Instead, adenine dispersion relaxation studies indicate enhanced millisecond time scale dynamics involving base pair opening. It can then be concluded that base pair opening is essential for epsilon-RT binding, because stabilization of the stem abolishes binding. We hypothesize that binding occurs by conformational capture of bases in the base pair open state. The unstable secondary structure of the apical stem-loop makes duck epsilon-RT binding unusual in light of recent classifications of RNA target interactions that assume stable secondary structures.

The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding.,Ampt KA, van der Werf RM, Nelissen FH, Tessari M, Wijmenga SS Biochemistry. 2009 Nov 10;48(44):10499-508. PMID:19817488^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ampt KA, van der Werf RM, Nelissen FH, Tessari M, Wijmenga SS. The unstable part of the apical stem of duck hepatitis B virus epsilon shows enhanced base pair opening but not pico- to nanosecond dynamics and is essential for reverse transcriptase binding. Biochemistry. 2009 Nov 10;48(44):10499-508. PMID:19817488 doi:10.1021/bi9011385

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2k5z"

@@ Line 4: / Line 4: @@
 <table><tr><td colspan='2'>[[2k5z]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K5Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K5Z FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oj7|2oj7]], [[2oj8|2oj8]], [[2k5y|2k5y]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2k5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k5z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k5z RCSB], [http://www.ebi.ac.uk/pdbsum/2k5z PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2k5z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k5z OCA], [http://pdbe.org/2k5z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2k5z RCSB], [http://www.ebi.ac.uk/pdbsum/2k5z PDBsum]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 14: / Line 14: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2k5z" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

2k5z

From Proteopedia

Revision as of 14:05, 10 September 2015

Solution structure and dynamics of the apical stem-loop of Duck hepatitis B virus

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox