1jb8: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1jb8.gif|left|200px]]<br /><applet load="1jb8" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1jb8, resolution 2.38&Aring;" />
'''The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation'''<br />


==Overview==
==The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation==
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.
<StructureSection load='1jb8' size='340' side='right'caption='[[1jb8]], [[Resolution|resolution]] 2.38&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
1JB8 is a [http://en.wikipedia.org/wiki/Protein_complex 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].  
</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>
 
<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>
==Reference==
</table>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12872000 12872000]
__TOC__
[[Category: Protein complex]]
</StructureSection>
[[Category: Dickerson, R E.]]
[[Category: Large Structures]]
[[Category: Han, G W.]]
[[Category: Dickerson RE]]
[[Category: Kopka, M L.]]
[[Category: Han GW]]
[[Category: Langs, D.]]
[[Category: Kopka ML]]
[[Category: dna/dna intercalation]]
[[Category: Langs D]]
[[Category: rna/dna hybrid]]
[[Category: rna/dna polypurine tract]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:20:40 2008''

Latest revision as of 10:38, 7 February 2024

The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular IntercalationThe Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation

Structural highlights

1jb8 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.38Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1jb8, resolution 2.38Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1jb8&oldid=4045212"