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1jb8

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[[Image:1jb8.gif|left|200px]]
 
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==The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation==
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The line below this paragraph, containing "STRUCTURE_1jb8", creates the "Structure Box" on the page.
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<StructureSection load='1jb8' size='340' side='right'caption='[[1jb8]], [[Resolution|resolution]] 2.38&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'>[[1jb8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JB8 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]] 2.38&#8491;</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=1jb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jb8 OCA], [https://pdbe.org/1jb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jb8 RCSB], [https://www.ebi.ac.uk/pdbsum/1jb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jb8 ProSAT]</span></td></tr>
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{{STRUCTURE_1jb8| PDB=1jb8 | SCENE= }}
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</table>
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__TOC__
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'''The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation'''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Dickerson RE]]
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==Overview==
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[[Category: Han GW]]
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An intermolecular intercalation of base pairs was found at the CA step in the I222 crystal structure of the RNA.DNA hybrid, r(CAAAGAAAAG).d(CTTTTCTTTG), which contains two-thirds of the polypurine tract sequence of HIV-1 with a substitution of cytosine for the initial adenine. This sequence crystallized in both P212121 and I222 space groups, with an rms difference of only 0.63 A between residues 3 to 18 of the two forms. P212121 and I222 helices are both A-like, but intercalation occurs only in the I222 crystal form. The present structure shows bases stacked in parallel rather than perpendicular as in intercalated DNA (I-DNA). The base intercalation is also different from zipper-like meshing of bases seen in the center of the crystal structure of d(GCGAAAGCT), which does not have Watson-Crick base pairing. The base-step intercalation seen here is reminiscent of domain swapping in proteins; therefore, we call this phenomenon "base-pair swapping." It involves a highly mobile CA step and seems to be sequence-specific and electrostatically stable without disrupting Watson-Crick interactions. It also exhibits a large rise concurrent with unwinding of the helix (low twist). We present a base-pair swapping dimer in nucleic acids.
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[[Category: Kopka ML]]
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[[Category: Langs D]]
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==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JB8 OCA].
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==Reference==
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Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping., Han GW, Kopka ML, Langs D, Sawaya MR, Dickerson RE, Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9214-9. Epub 2003 Jul 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12872000 12872000]
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[[Category: Dickerson, R E.]]
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[[Category: Han, G W.]]
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[[Category: Kopka, M L.]]
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[[Category: Langs, D.]]
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[[Category: Dna/dna intercalation]]
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[[Category: Rna/dna hybrid]]
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[[Category: Rna/dna polypurine tract]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 21:00:29 2008''
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The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation

PDB ID 1jb8

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