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| - | [[Image:1jb8.gif|left|200px]] | |
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| - | {{Structure
| + | ==The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation== |
| - | |PDB= 1jb8 |SIZE=350|CAPTION= <scene name='initialview01'>1jb8</scene>, resolution 2.38Å
| + | <StructureSection load='1jb8' size='340' side='right'caption='[[1jb8]], [[Resolution|resolution]] 2.38Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jb8 OCA], [http://www.ebi.ac.uk/pdbsum/1jb8 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jb8 RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Dickerson RE]] |
| - | '''The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation'''
| + | [[Category: Han GW]] |
| - | | + | [[Category: Kopka ML]] |
| - | | + | [[Category: Langs D]] |
| - | ==Overview==
| + | |
| - | 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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| - | ==About this Structure==
| + | |
| - | 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].
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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: Protein complex]] | + | |
| - | [[Category: Dickerson, R E.]] | + | |
| - | [[Category: Han, G W.]] | + | |
| - | [[Category: Kopka, M L.]] | + | |
| - | [[Category: Langs, D.]] | + | |
| - | [[Category: dna/dna intercalation]]
| + | |
| - | [[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 Sun Mar 30 21:31:08 2008''
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