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| - | [[Image:1cw9.gif|left|200px]] | |
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| - | {{Structure
| + | ==DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE== |
| - | |PDB= 1cw9 |SIZE=350|CAPTION= <scene name='initialview01'>1cw9</scene>, resolution 1.55Å
| + | <StructureSection load='1cw9' size='340' side='right'caption='[[1cw9]], [[Resolution|resolution]] 1.55Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</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=G47:N2-ETHANETHIOL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE'>G47</scene>
| + | <table><tr><td colspan='2'>[[1cw9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CW9 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]] 1.55Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=G47:N2-ETHANETHIOL-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>G47</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cw9 OCA], [https://pdbe.org/1cw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1cw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cw9 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1cw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cw9 OCA], [http://www.ebi.ac.uk/pdbsum/1cw9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1cw9 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE'''
| + | [[Category: Erlanson DA]] |
| - | | + | [[Category: Joshua-Tor L]] |
| - | | + | [[Category: Verdine GL]] |
| - | ==Overview==
| + | [[Category: Van Aalten DMF]] |
| - | The response of double-helical DNA to torsional stress may be a driving force for many processes acting on DNA. The 1.55-A crystal structure of a duplex DNA oligonucleotide d(CCAGGCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine bases depicts how the duplex can accommodate such torsional stress. We have captured in the same crystal two rather different conformational states. One duplex contains a strained crosslink that is stabilized by calcium ion binding in the major groove, directly opposite the crosslink. For the other duplex, the strain in the crosslink is relieved through partial rupture of a base pair and partial extrusion of a cytosine accompanied by helix bending. The sequence used is the target sequence for the HaeIII methylase, and this partially flipped cytosine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics simulations of these structures show an increased mobility for the partially flipped-out cytosine.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1CW9 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=1CW9 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | A structural snapshot of base-pair opening in DNA., van Aalten DM, Erlanson DA, Verdine GL, Joshua-Tor L, Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11809-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10518532 10518532]
| + | |
| - | [[Category: Protein complex]]
| + | |
| - | [[Category: Aalten, D. M. F van.]] | + | |
| - | [[Category: Erlanson, D. A.]] | + | |
| - | [[Category: Joshua-Tor, L.]] | + | |
| - | [[Category: Verdine, G. L.]] | + | |
| - | [[Category: base-pair opening]] | + | |
| - | [[Category: crosslinked double-helical dna]]
| + | |
| - | [[Category: partial base flipping.]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:29:49 2008''
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