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3ssf

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[[Image:3ssf.png|left|200px]]
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==Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A resolution.==
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<StructureSection load='3ssf' size='340' side='right' caption='[[3ssf]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3ssf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SSF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SSF FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pjo|1pjo]], [[1pjg|1pjg]], [[1jb8|1jb8]], [[1g4q|1g4q]]</td></tr>
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<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=3ssf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ssf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ssf RCSB], [http://www.ebi.ac.uk/pdbsum/3ssf PDBsum]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 A resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (at nucleotides 1-2 and 6-8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I((1-2), (6-8)), 25% of the RNA sugars have the C2'-exo pucker and the rest have the expected C3'-endo pucker. The II(1-2) and II(6-8) conformations of the RNA strand have one sugar with the C2'-exo pucker. None of the ribose rings exist in the C2'-endo form, in contrast to a previous report which postulated a C2'-endo ribose as a key structural element of the PPT. The widths of the minor groove for conformations I((1-2), (6-8)) and II((1-2), (6-8)) of the RNA strand are 9.2-10.5 and 9.4-10.7 A, respectively. Both ranges are very close to the intervals accepted for A-form RNA duplexes. On the opposing DNA primer strand most of the sugars are C3'-endo, except for the 3'-terminal sugars, which are C2'-endo (T22) or O4'-endo (T23 and A24). The duplex includes a noncanonical u1(anti).A24(syn) base interaction with only one hydrogen bond between the bases. This noncanonical base interaction at the 5'-end of the template distorts the values of the helical parameters of the adjacent base pair.
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Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 A resolution.,Drozdzal P, Michalska K, Kierzek R, Lomozik L, Jaskolski M Acta Crystallogr D Biol Crystallogr. 2012 Feb;68(Pt 2):169-75. Epub 2012 Jan 6. PMID:22281746<ref>PMID:22281746</ref>
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The line below this paragraph, containing "STRUCTURE_3ssf", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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{{STRUCTURE_3ssf| PDB=3ssf | SCENE= }}
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===Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A resolution.===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_22281746}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 22281746 is the PubMed ID number.
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</StructureSection>
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[[Category: Drozdzal, P]]
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{{ABSTRACT_PUBMED_22281746}}
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[[Category: Jaskolski, M]]
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[[Category: Kierzek, R]]
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==About this Structure==
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[[Category: Lomozik, L]]
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[[3ssf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SSF OCA].
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[[Category: Michalska, K]]
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==Reference==
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<ref group="xtra">PMID:022281746</ref><references group="xtra"/>
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[[Category: Drozdzal, P.]]
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[[Category: Jaskolski, M.]]
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[[Category: Kierzek, R.]]
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[[Category: Lomozik, L.]]
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[[Category: Michalska, K.]]
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[[Category: Reverse transcription]]
[[Category: Reverse transcription]]
[[Category: Rna-dna complex]]
[[Category: Rna-dna complex]]
[[Category: Rna-dna hybrid]]
[[Category: Rna-dna hybrid]]

Revision as of 09:19, 4 January 2015

Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A resolution.

3ssf, resolution 1.60Å

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