1uhx

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(New page: 200px<br /><applet load="1uhx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1uhx, resolution 2.0&Aring;" /> '''Crystal structure of ...)
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[[Image:1uhx.gif|left|200px]]<br /><applet load="1uhx" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1uhx, resolution 2.0&Aring;" />
 
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'''Crystal structure of d(GCGAGAGC): the base-intercalated duplex'''<br />
 
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==Overview==
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==Crystal structure of d(GCGAGAGC): the base-intercalated duplex==
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DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a, base-intercalated (zipper-like) duplex in the crystalline state. To, investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined, by X-ray crystallography. In the respective crystals, the two octamers, related by a crystallographic two-fold symmetry are aligned in an, anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th, residue is mutated with other bases. The sheared G3:A6 pair formation, makes the two phosphate backbones closer and facilitates formation of the, A-X*-X-A* base-intercalated motif. The three duplexes are assembled around, the three-fold axis, and their 3rd and 4th residues are bound to the, hexamine cobalt chloride. The central 5th residues are bound to another, cation.
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<StructureSection load='1uhx' size='340' side='right'caption='[[1uhx]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1uhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UHX 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&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></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=1uhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uhx OCA], [https://pdbe.org/1uhx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uhx RCSB], [https://www.ebi.ac.uk/pdbsum/1uhx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uhx ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.
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==About this Structure==
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X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.,Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:14646150<ref>PMID:14646150</ref>
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1UHX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG, CL, NA 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=1UHX OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue., Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A, J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14646150 14646150]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1uhx" style="background-color:#fffaf0;"></div>
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[[Category: Fujita, K.]]
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== References ==
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[[Category: Kondo, J.]]
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<references/>
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[[Category: Sunami, T.]]
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__TOC__
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[[Category: Takenaka, A.]]
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</StructureSection>
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[[Category: Umeda, S.I.]]
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[[Category: Large Structures]]
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[[Category: CL]]
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[[Category: Fujita K]]
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[[Category: MG]]
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[[Category: Kondo J]]
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[[Category: NA]]
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[[Category: Sunami T]]
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[[Category: NCO]]
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[[Category: Takenaka A]]
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[[Category: base-intercalated duplex]]
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[[Category: Umeda SI]]
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[[Category: base-intercalated motif]]
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[[Category: deoxyribonucleic acid]]
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[[Category: dna]]
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[[Category: sheared g:a pair]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:01:19 2007''
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Current revision

Crystal structure of d(GCGAGAGC): the base-intercalated duplex

PDB ID 1uhx

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