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[[Image:1m5l.jpg|left|200px]]<br /><applet load="1m5l" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1m5l" />
'''Structure of wild-type and mutant internal loops from the SL-1 domain of the HIV-1 packaging signal'''<br />


==Overview==
==Structure of wild-type and mutant internal loops from the SL-1 domain of the HIV-1 packaging signal==
The packaging signal (Psi) of the human immunodeficiency virus type 1, (HIV-1) enables encapsidation of the full-length genomic RNA against a, background of a vast excess of cellular mRNAs. The core HIV-1 Psi is, approximately 109 nucleotides and contains sequences critical for viral, genomic dimerisation and splicing, in addition to the packaging signal. It, consists of a series of stem-loops (termed SL-1 to SL-4), which can be, arranged in a cloverleaf secondary structure. Using a combination of NMR, spectroscopy, UV melting experiments, molecular modeling and phylogenetic, analyses, we have explored the structure of two conserved internal loops, proximal to the palindromic sequence of SL-1. Internal loop A, composed of, six purines, forms a flexible structure that is strikingly similar to the, Rev responsive element motif when bound to Rev protein. This result, suggests that it may function as a protein-binding site. The absolutely, conserved four-purine internal loop B is instead conformationally and, thermodynamically unstable, and exhibits multiple conformations in, solution. By introducing a double AGG to GGA mutation within this loop, its conformation is stabilised to form a new intra-molecular G:A:G, base-triplet. The structure of the GGA mutant explains the relative, instability of the wild-type loop. In a manner analogous to SL-3, we, propose that conformational flexibility at this site may facilitate, melting of the structure during Gag protein capture or genomic RNA, dimerisation.
<StructureSection load='1m5l' size='340' side='right'caption='[[1m5l]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1m5l]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5L 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=1m5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5l OCA], [https://pdbe.org/1m5l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5l RCSB], [https://www.ebi.ac.uk/pdbsum/1m5l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5l ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The packaging signal (Psi) of the human immunodeficiency virus type 1 (HIV-1) enables encapsidation of the full-length genomic RNA against a background of a vast excess of cellular mRNAs. The core HIV-1 Psi is approximately 109 nucleotides and contains sequences critical for viral genomic dimerisation and splicing, in addition to the packaging signal. It consists of a series of stem-loops (termed SL-1 to SL-4), which can be arranged in a cloverleaf secondary structure. Using a combination of NMR spectroscopy, UV melting experiments, molecular modeling and phylogenetic analyses, we have explored the structure of two conserved internal loops proximal to the palindromic sequence of SL-1. Internal loop A, composed of six purines, forms a flexible structure that is strikingly similar to the Rev responsive element motif when bound to Rev protein. This result suggests that it may function as a protein-binding site. The absolutely conserved four-purine internal loop B is instead conformationally and thermodynamically unstable, and exhibits multiple conformations in solution. By introducing a double AGG to GGA mutation within this loop, its conformation is stabilised to form a new intra-molecular G:A:G base-triplet. The structure of the GGA mutant explains the relative instability of the wild-type loop. In a manner analogous to SL-3, we propose that conformational flexibility at this site may facilitate melting of the structure during Gag protein capture or genomic RNA dimerisation.


==About this Structure==
Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal.,Greatorex J, Gallego J, Varani G, Lever A J Mol Biol. 2002 Sep 20;322(3):543-57. PMID:12225748<ref>PMID:12225748</ref>
1M5L is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5L OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal., Greatorex J, Gallego J, Varani G, Lever A, J Mol Biol. 2002 Sep 20;322(3):543-57. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12225748 12225748]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1m5l" style="background-color:#fffaf0;"></div>
[[Category: Gallego, J.]]
== References ==
[[Category: Greatorex, J.]]
<references/>
[[Category: Lever, A.]]
__TOC__
[[Category: Varani, G.]]
</StructureSection>
[[Category: base triplet]]
[[Category: Large Structures]]
[[Category: hiv]]
[[Category: Gallego J]]
[[Category: internal loop]]
[[Category: Greatorex J]]
[[Category: packaging signal]]
[[Category: Lever A]]
[[Category: s-turn]]
[[Category: Varani G]]
[[Category: sl-1]]
 
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