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.


1l4j

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1l4j.gif|left|200px]]
+
{{Seed}}
 +
[[Image:1l4j.png|left|200px]]
<!--
<!--
Line 9: Line 10:
{{STRUCTURE_1l4j| PDB=1l4j | SCENE= }}
{{STRUCTURE_1l4j| PDB=1l4j | SCENE= }}
-
'''Holliday Junction TCGGTACCGA with Na and Ca Binding Sites.'''
+
===Holliday Junction TCGGTACCGA with Na and Ca Binding Sites.===
-
==Overview==
+
<!--
-
The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na(+) and Ca(2+), and separately with Sr(2+) to resolutions of 1.85A and 1.65A, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na(+) sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca(2+) sites in the same structure are at the CG/CG steps in the minor groove. The Sr(2+) ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr(2+) derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4 degrees in the Ca(2+) and Na(+) containing structure, and 13.4 degrees in the Sr(2+) containing structure. The crossover angles at the junction are 39.3 degrees and 43.3 degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3A is observed for the Sr(2+) containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction.
+
The line below this paragraph, {{ABSTRACT_PUBMED_12614611}}, adds the Publication Abstract to the page
 +
(as it appears on PubMed at http://www.pubmed.gov), where 12614611 is the PubMed ID number.
 +
-->
 +
{{ABSTRACT_PUBMED_12614611}}
==About this Structure==
==About this Structure==
Line 25: Line 29:
[[Category: Thorpe, J H.]]
[[Category: Thorpe, J H.]]
[[Category: Holliday junction]]
[[Category: Holliday junction]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:32:06 2008''
+
 
 +
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 11:41:33 2008''

Revision as of 08:41, 2 July 2008

Image:1l4j.png

Template:STRUCTURE 1l4j

Holliday Junction TCGGTACCGA with Na and Ca Binding Sites.

Template:ABSTRACT PUBMED 12614611

About this Structure

Full crystallographic information is available from OCA.

Reference

Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4)., Thorpe JH, Gale BC, Teixeira SC, Cardin CJ, J Mol Biol. 2003 Mar 14;327(1):97-109. PMID:12614611

Page seeded by OCA on Wed Jul 2 11:41:33 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l4j"
Personal tools