1jrn
From Proteopedia
(New page: 200px<br /><applet load="1jrn" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jrn, resolution 2.0Å" /> '''Orthorhombic form of ...) |
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| - | [[Image:1jrn.gif|left|200px]]<br /><applet load="1jrn" size=" | + | [[Image:1jrn.gif|left|200px]]<br /><applet load="1jrn" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1jrn, resolution 2.0Å" /> | caption="1jrn, resolution 2.0Å" /> | ||
'''Orthorhombic form of Oxytricha telomeric DNA at 2.0A'''<br /> | '''Orthorhombic form of Oxytricha telomeric DNA at 2.0A'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structures of the potassium-containing quadruplex formed from | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1JRN is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with K as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1JRN 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=1JRN OCA]. |
==Reference== | ==Reference== | ||
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] | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Haider, S | + | [[Category: Haider, S M.]] |
[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
[[Category: Parkinson, G.]] | [[Category: Parkinson, G.]] | ||
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[[Category: oxytricha]] | [[Category: oxytricha]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:25:57 2008'' |
Revision as of 11:25, 21 February 2008
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Orthorhombic form of Oxytricha telomeric DNA at 2.0A
Overview
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.
About this Structure
1JRN is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
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:12079378
Page seeded by OCA on Thu Feb 21 13:25:57 2008
Categories: Protein complex | Haider, S M. | Neidle, S. | Parkinson, G. | K | G-quartets | Oxytricha
