1jb8: Difference between revisions
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[[Image:1jb8.gif|left|200px]] | [[Image:1jb8.gif|left|200px]] | ||
'''The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation''' | {{Structure | ||
|PDB= 1jb8 |SIZE=350|CAPTION= <scene name='initialview01'>1jb8</scene>, resolution 2.38Å | |||
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'''The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1JB8 is a [ | 1JB8 is a [[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=1JB8 OCA]. | ||
==Reference== | ==Reference== | ||
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:// | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Dickerson, R E.]] | [[Category: Dickerson, R E.]] | ||
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[[Category: rna/dna polypurine tract]] | [[Category: rna/dna polypurine tract]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:01:05 2008'' | ||
Revision as of 13:01, 20 March 2008
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The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation
OverviewOverview
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.
About this StructureAbout this Structure
1JB8 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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:12872000
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