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.


1jpq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:41, 7 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1jpq.gif|left|200px]]<br /><applet load="1jpq" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1jpq, resolution 1.6&Aring;" />
 
-
'''Crystal Structure of the Oxytricha Telomeric DNA at 1.6A'''<br />
 
-
==Overview==
+
==Crystal Structure of the Oxytricha Telomeric DNA at 1.6A==
-
The crystal structures of the potassium-containing quadruplex formed from the Oxytricha nova sequence d(GGGGTTTTGGGG) are reported, in two space groups, the orthorhombic P2(1)2(1)2(1) and the trigonal P3(2)21, which diffract to 2.0 A and 1.49 A, respectively. The orthorhombic form contains two independent quadruplexes in the asymmetric unit, and the trigonal form contains one. All three of these quadruplexes adopt an identical fold, with two strands forming an antiparallel diagonal arrangement. This is identical with that observed previously in NMR studies of the native sodium and potassium forms, and a crystallographic analysis of it complexed with an O. nova protein. The present analysis demonstrates that the native structure is the same in solution and in the crystalline state and, moreover, that the nature of the counter-ion does not affect the overall fold of this quadruplex. The analysis corrects an earlier crystallographic study of this quadruplex. The conformation of the tetra-thymine loop is described in detail, which involves the third thymine base folding back to interact with the first thymine base. The water networks in the grooves and loops are described and, in particular, the ability of water molecules to form a continuous spine of hydration in the narrow groove is detailed. Each quadruplex has five potassium ions organised in a linear channel, with square antiprismatic coordination to each ion from oxygen atoms.
+
<StructureSection load='1jpq' size='340' side='right'caption='[[1jpq]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1jpq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JPQ FirstGlance]. <br>
-
1JPQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=K:'>K</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JPQ 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]] 1.6&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=1jpq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jpq OCA], [https://pdbe.org/1jpq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jpq RCSB], [https://www.ebi.ac.uk/pdbsum/1jpq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jpq ProSAT]</span></td></tr>
-
Crystal structure of the potassium form of an Oxytricha nova G-quadruplex., Haider S, Parkinson GN, Neidle S, J Mol Biol. 2002 Jul 5;320(2):189-200. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12079378 12079378]
+
</table>
-
[[Category: Protein complex]]
+
__TOC__
-
[[Category: Haider, S M.]]
+
</StructureSection>
-
[[Category: Neidle, S.]]
+
[[Category: Large Structures]]
-
[[Category: Parkinson, G.]]
+
[[Category: Haider SM]]
-
[[Category: K]]
+
[[Category: Neidle S]]
-
[[Category: g-quartets]]
+
[[Category: Parkinson G]]
-
[[Category: oxytricha]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:25:17 2008''
+

Current revision

Crystal Structure of the Oxytricha Telomeric DNA at 1.6A

PDB ID 1jpq

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/1jpq"
Personal tools