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.


1f6e

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1f6e" size="450" color="white" frame="true" align="right" spinBox="true" caption="1f6e, resolution 2.0&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
Current revision (07:11, 7 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1f6e.gif|left|200px]]<br /><applet load="1f6e" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1f6e, resolution 2.0&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF THE A-DNA HEXAMER GGCGM5CC'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF THE A-DNA HEXAMER GGCGM5CC==
-
Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is, shown here to induce a novel extended and eccentric double helix, which we, call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases, perpendicular to the helix axis. However, the 3'-endo sugar conformation, gives the characteristic deep major groove and shallow minor groove of, A-DNA. Also, if allowed to crystallize for a period of time longer than, that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the, transition to A-DNA. Thus, the structures presented here chart a, crystallographic pathway from B-DNA to A-DNA through the E-DNA, intermediate in a single sequence. The E-DNA surface is highly accessible, to solvent, with waters in the major groove sitting on exposed faces of, the stacked nucleotides. We suggest that the geometry of the waters and, the stacked base pairs would promote the spontaneous deamination of, 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base, pairs.
+
<StructureSection load='1f6e' size='340' side='right'caption='[[1f6e]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1f6e]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6E FirstGlance]. <br>
-
1F6E 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=1F6E 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&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6e OCA], [https://pdbe.org/1f6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6e RCSB], [https://www.ebi.ac.uk/pdbsum/1f6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6e ProSAT]</span></td></tr>
-
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination., Vargason JM, Eichman BF, Ho PS, Nat Struct Biol. 2000 Sep;7(9):758-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10966645 10966645]
+
</table>
-
[[Category: Protein complex]]
+
__TOC__
-
[[Category: Eichman, B.F.]]
+
</StructureSection>
-
[[Category: Ho, P.S.]]
+
[[Category: Large Structures]]
-
[[Category: Vargason, J.M.]]
+
[[Category: Eichman BF]]
-
[[Category: a-dna]]
+
[[Category: Ho PS]]
-
[[Category: double helix]]
+
[[Category: Vargason JM]]
-
[[Category: e-dna]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:21:44 2007''
+

Current revision

CRYSTAL STRUCTURE OF THE A-DNA HEXAMER GGCGM5CC

PDB ID 1f6e

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1f6e"
Personal tools