1ue2: Difference between revisions

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New page: left|200px<br /><applet load="1ue2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ue2, resolution 1.4Å" /> '''Crystal structure of ...
 
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[[Image:1ue2.gif|left|200px]]<br /><applet load="1ue2" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ue2, resolution 1.4&Aring;" />
'''Crystal structure of d(GI5CGAAAGCT)'''<br />


==Overview==
==Crystal structure of d(GC38GAAAGCT)==
A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin, structure on the basis of its extraordinary properties, has been X-ray, analyzed. Two octamers related by a crystallographic twofold symmetry are, aligned in an antiparallel fashion and associate to form a duplex, which, is maintained by two Watson-Crick G.C base pairs and a subsequent sheared, G.A pair at both ends. The central two A residues are free from base-pair, formation. The corresponding base moieties of the two strands are, intercalated and stacked on each other, forming a long column of, G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*), (asterisks indicate the counter-strand). The Watson-Crick and major-groove, sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to, those found in the nonamers d(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), the, base-intercalated duplex may be a stable form of the specific sequence., Electrophoresis results suggest that the octamer has two states, monomeric, and dimeric, in solution depending on the Mg(2+) concentration. The, present duplex is preferred under the crystallization conditions, which, correspond to physiologically allowed conditions.
<StructureSection load='1ue2' size='340' side='right'caption='[[1ue2]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ue2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UE2 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C38:5-IODO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>C38</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></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=1ue2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ue2 OCA], [https://pdbe.org/1ue2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ue2 RCSB], [https://www.ebi.ac.uk/pdbsum/1ue2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ue2 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G.C base pairs and a subsequent sheared G.A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (asterisks indicate the counter-strand). The Watson-Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.


==About this Structure==
Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.,Sunami T, Kondo J, Hirao I, Watanabe K, Miura KI, Takenaka A Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):90-6. Epub 2003 Dec, 18. PMID:14684897<ref>PMID:14684897</ref>
1UE2 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CL, MG and NCO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UE2 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure., Sunami T, Kondo J, Hirao I, Watanabe K, Miura KI, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):90-6. Epub 2003 Dec, 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14684897 14684897]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1ue2" style="background-color:#fffaf0;"></div>
[[Category: Hirao, I.]]
== References ==
[[Category: Kondo, J.]]
<references/>
[[Category: Miura, K.]]
__TOC__
[[Category: Sunami, T.]]
</StructureSection>
[[Category: Takenaka, A.]]
[[Category: Large Structures]]
[[Category: Watanaba, K.]]
[[Category: Hirao I]]
[[Category: CL]]
[[Category: Kondo J]]
[[Category: MG]]
[[Category: Miura K]]
[[Category: NCO]]
[[Category: Sunami T]]
[[Category: base-intercalated duplex]]
[[Category: Takenaka A]]
[[Category: dna]]
[[Category: Watanaba K]]
[[Category: mini-hairpin structure]]
[[Category: sheared g:a pair]]
[[Category: zipper-like duplex]]
 
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Latest revision as of 06:05, 5 July 2023

Crystal structure of d(GC38GAAAGCT)

1ue2, resolution 1.40Å

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