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1k9w

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[[Image:1k9w.gif|left|200px]]
 
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==HIV-1(MAL) RNA Dimerization Initiation Site==
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The line below this paragraph, containing "STRUCTURE_1k9w", creates the "Structure Box" on the page.
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<StructureSection load='1k9w' size='340' side='right'caption='[[1k9w]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1k9w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K9W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K9W FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1k9w| PDB=1k9w | SCENE= }}
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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=1k9w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k9w OCA], [https://pdbe.org/1k9w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k9w RCSB], [https://www.ebi.ac.uk/pdbsum/1k9w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k9w ProSAT]</span></td></tr>
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</table>
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'''HIV-1(MAL) RNA Dimerization Initiation Site'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Dumas P]]
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We describe the crystal structures of the RNA dimerization initiation sites (DIS) of HIV-1 subtypes A and B. Both molecules adopt a hairpin conformation, with loop sequences consisting of 272-AGGUGCACA-280 and 272-AAGCGCGCA-280, respectively. This includes a six-base self-complementary stretch (underlined) that allows homodimerization through the formation of a loop-loop, or 'kissing-loop', complex. The DISs for the two sequences have identical conformations, and the two interacting hairpins show a perfect coaxial alignment. The conserved purines, A272 and R273, are stacked in a bulged-out conformation and symmetrically join the upward and downward strands of each hairpin by crossing the helix major groove. There is good agreement between these structures and previous results from chemical probing in solution, as well as with differences in magnesium dependence for dimerization. The overall shape of the kissing-loop complex is very similar to that of the previously determined subtype A DIS duplex form. Unexpectedly, the purine R273 is the only base seen at a different position and is responsible for the difference in topology between the two forms. We propose that the transition from kissing-loop duplex could occur by a recombination mechanism based on symmetrical chain cleavage at R273 of each hairpin and subsequent cross-religation, rather than by base-pair melting and subsequent reannealing.
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[[Category: Ehresmann B]]
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[[Category: Ehresmann C]]
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==About this Structure==
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[[Category: Ennifar E]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K9W OCA].
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[[Category: Walter P]]
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==Reference==
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Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site., Ennifar E, Walter P, Ehresmann B, Ehresmann C, Dumas P, Nat Struct Biol. 2001 Dec;8(12):1064-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11702070 11702070]
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[[Category: Dumas, P.]]
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[[Category: Ehresmann, B.]]
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[[Category: Ehresmann, C.]]
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[[Category: Ennifar, E.]]
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[[Category: Walter, P.]]
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[[Category: Hairpin]]
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[[Category: Hiv]]
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[[Category: Rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:29:13 2008''
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Current revision

HIV-1(MAL) RNA Dimerization Initiation Site

PDB ID 1k9w

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