This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

167d

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/167d"

Categories: Large Structures | Dickerson RE | Goodsell DS | Kaczor-Grzeskowiak M

@@ Line 1: / Line 1: @@
-[[Image:167d.gif|left|200px]]<br /><applet load="167d" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="167d, resolution 2.300&Aring;" />
-'''THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS'''<br />
-==Overview==
+==THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS==
-The single-crystal X-ray analysis of trigonal C-C-A-T-T-A-A-T-G-G, and its, comparison with orthorhombic C-G-A-T-T-A-A-T-C-G, have shown that the, A-T-T-A-A-T sequence has limited polymorphism under the influence of, packing forces from neighboring molecules in the crystal. The T-A step is, intrinsically variable. It is not inconsistent with a large propeller, twist, a narrow minor groove, and a single spine of hydration, as has, sometimes been claimed on theoretical grounds. The T-A step does show a, persistent positive roll, in a direction that compresses the major groove, and this may be a significant factor in macroscopic DNA curvature induced, by phased A-tracts. A-tracts, as understood in this paper, include A-A and, A-T steps, but not the T-A step, which is disruptive. Three conclusions, regarding A-tract-induced curvature can be drawn from this and other X-ray, crystal structure analyses, and from key gel retardation experiments: (1), The A-tract bending model is disqualified on two grounds: (i) tilt-wedge, bending within A-tracts is incompatible with the observed direction of, curvature; (ii) roll-wedge bending within A-tracts is contradicted by, every crystal structure analysis, and is inconsistent with gel retardation, results for (G-C-A-A-A-A-T-T-T-T)n and for (A-A-A-A-A-T-T-T-T-T)n. (2) The, junction bend model is contradicted by crystallography because: (i) the, inclination of base-pairs does not change between A-tract and non-A-tract, regions of helix; and (ii) the observed bends at GC/AT junctions are, roll-wedge bends, not tilt-wedge as the junction bend model demands. (3), The non-A-tract bending model is consistent with both gel retardation data, and with X-ray crystallography, and must be regarded as the only, consistent model for A-tract bending.
+<StructureSection load='167d' size='340' side='right'caption='[[167d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[167d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=167D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=167D FirstGlance]. <br>
-D 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=167D 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]] 2.3&#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=167d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=167d OCA], [https://pdbe.org/167d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=167d RCSB], [https://www.ebi.ac.uk/pdbsum/167d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=167d ProSAT]</span></td></tr>
-==Reference==
+</table>
-The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps., Goodsell DS, Kaczor-Grzeskowiak M, Dickerson RE, J Mol Biol. 1994 May 27;239(1):79-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8196049 8196049]
+__TOC__
-[[Category: Protein complex]]
+</StructureSection>
-[[Category: Dickerson, R.E.]]
+[[Category: Large Structures]]
-[[Category: Goodsell, D.S.]]
+[[Category: Dickerson RE]]
-[[Category: Kaczor-Grzeskowiak, M.]]
+[[Category: Goodsell DS]]
-[[Category: b-dna]]
+[[Category: Kaczor-Grzeskowiak M]]
-[[Category: double helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:02:41 2007''

167d

From Proteopedia

Current revision

THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS

Structural highlights

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox