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| [[Image:1esy.gif|left|200px]]<br />
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| <applet load="1esy" size="450" color="white" frame="true" align="right" spinBox="true"
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| caption="1esy" />
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| '''NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM'''<br />
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| ==Overview== | | ==NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM== |
| The genome of the human immunodeficiency virus type-1 (HIV-1) contains a, stretch of approximately 120 nucleotides known as the psi-site that is, essential for RNA packaging during virus assembly. These nucleotides have, been proposed to form four stem-loops (SL1-SL4) that have both independent, and overlapping functions. Stem-loop SL2 is important for efficient, recognition and packaging of the full-length, unspliced viral genome, and, also contains the major splice-donor site (SD) for mRNA splicing. We have, determined the structure of the 19-residue SL2 oligoribonucleotide by, heteronuclear NMR methods. The structure is generally consistent with the, most recent of two earlier secondary structure predictions, with residues, G1-G2-C3-G4 and C6-U7 forming standard Watson Crick base-pairs with, self-complementary residues C16-G17-C18-C19 and A12-G13, respectively., However, residue A15, which is located near the center of the stem, does, not form a predicted bulge, and residues A5 and U14 do not form an, expected Watson-Crick base-pair. Instead, these residues form a novel, A5-U14-A15 base-triple that appears to be stabilized by hydrogen bonds, from A15-H61 and -H62 to A5-N1 and U14-O2, respectively; from A5-H61 to, U14-O2, and from C16-H42 to U14-O2'. A kink in the backbone allows the, aromatic rings of the sequential U14-A15 residues to be approximately, co-planar, adopting a stable "platform motif" that is structurally similar, to the A-A (adenosine) platforms observed in the P4-P6 ribozyme domain of, the Tetrahymena group I intron. Platform motifs generally function in RNA, by mediating long-range interactions, and it is therefore possible that, the A-U-A base-triple platform mediates long-range interactions that, either stabilize the psi-RNA or facilitate splicing and/or packaging., Residue G8 of the G8-G9-U10-G11 tetraloop is stacked above the U7-A12, base-pair, and the remaining tetraloop residues are disordered and, available for potential interactions with either other RNA or protein, components.
| | <StructureSection load='1esy' size='340' side='right'caption='[[1esy]]' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1esy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ESY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ESY FirstGlance]. <br> |
| 1ESY 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ESY OCA].
| | </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=1esy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1esy OCA], [https://pdbe.org/1esy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1esy RCSB], [https://www.ebi.ac.uk/pdbsum/1esy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1esy ProSAT]</span></td></tr> |
| ==Reference== | | </table> |
| NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novel A-U-A base-triple platform., Amarasinghe GK, De Guzman RN, Turner RB, Summers MF, J Mol Biol. 2000 May 26;299(1):145-56. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10860728 10860728]
| | __TOC__ |
| [[Category: Protein complex]] | | </StructureSection> |
| [[Category: Amarasinghe, G.K.]] | | [[Category: Human immunodeficiency virus 1]] |
| [[Category: Guzman, R.N.De.]]
| | [[Category: Large Structures]] |
| [[Category: Summers, M.F.]]
| | [[Category: Amarasinghe GK]] |
| [[Category: Turner, R.B.]] | | [[Category: De Guzman RN]] |
| [[Category: hiv-1]] | | [[Category: Summers MF]] |
| [[Category: nmr structure]] | | [[Category: Turner RB]] |
| [[Category: platform motif]] | |
| [[Category: rna]] | |
| [[Category: splice-donor site]] | |
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| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 14:01:34 2007''
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