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1esy

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[[Image:1esy.gif|left|200px]]<br /><applet load="1esy" size="350" 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==
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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==
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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.
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<StructureSection load='1esy' size='340' side='right'caption='[[1esy]]' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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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://oca.weizmann.ac.il/oca-bin/ocashort?id=1ESY OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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==Reference==
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</table>
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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., 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]
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__TOC__
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[[Category: Protein complex]]
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</StructureSection>
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[[Category: Amarasinghe, G K.]]
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[[Category: Human immunodeficiency virus 1]]
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[[Category: Guzman, R N.De.]]
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[[Category: Large Structures]]
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[[Category: Summers, M F.]]
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[[Category: Amarasinghe GK]]
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[[Category: Turner, R B.]]
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[[Category: De Guzman RN]]
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[[Category: hiv-1]]
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[[Category: Summers MF]]
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[[Category: nmr structure]]
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[[Category: Turner RB]]
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[[Category: platform motif]]
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[[Category: rna]]
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[[Category: splice-donor site]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:31:10 2008''
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Current revision

NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM

PDB ID 1esy

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