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| - | [[Image:1ekw.gif|left|200px]] | |
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| - | <!--
| + | ==NMR STRUCTURE OF A DNA THREE-WAY JUNCTION== |
| - | The line below this paragraph, containing "STRUCTURE_1ekw", creates the "Structure Box" on the page.
| + | <StructureSection load='1ekw' size='340' side='right'caption='[[1ekw]]' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1ekw]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EKW FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1ekw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ekw OCA], [https://pdbe.org/1ekw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ekw RCSB], [https://www.ebi.ac.uk/pdbsum/1ekw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ekw ProSAT]</span></td></tr> |
| - | {{STRUCTURE_1ekw| PDB=1ekw | SCENE= }}
| + | </table> |
| - | | + | __TOC__ |
| - | '''NMR STRUCTURE OF A DNA THREE-WAY JUNCTION'''
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | | + | [[Category: Donne D]] |
| - | ==Overview== | + | [[Category: Gorenstein DG]] |
| - | Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (approximately 60 degrees) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (+/- 20 degrees) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method.
| + | [[Category: Leontis NB]] |
| - | | + | [[Category: Luxon BA]] |
| - | ==About this Structure== | + | [[Category: Thiviyanathan V]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKW OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY., Thiviyanathan V, Luxon BA, Leontis NB, Illangasekare N, Donne DG, Gorenstein DG, J Biomol NMR. 1999 Jul;14(3):209-21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10481274 10481274]
| + | |
| - | [[Category: Donne, D.]] | + | |
| - | [[Category: Gorenstein, D G.]] | + | |
| - | [[Category: Leontis, N B.]] | + | |
| - | [[Category: Luxon, B A.]] | + | |
| - | [[Category: Thiviyanathan, V.]] | + | |
| - | [[Category: Dna]] | + | |
| - | [[Category: Three-way-junction]] | + | |
| - | [[Category: Unpaired base]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:13:29 2008''
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