1vj4
From Proteopedia
(New page: 200px<br /> <applet load="1vj4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vj4, resolution 1.800Å" /> '''SEQUENCE-DEPENDENT...) |
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| - | [[Image:1vj4.gif|left|200px]]<br /> | + | [[Image:1vj4.gif|left|200px]]<br /><applet load="1vj4" size="350" color="white" frame="true" align="right" spinBox="true" |
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caption="1vj4, resolution 1.800Å" /> | caption="1vj4, resolution 1.800Å" /> | ||
'''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)'''<br /> | '''SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structures of the synthetic self-complementary octamer | + | The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions. |
==About this Structure== | ==About this Structure== | ||
| - | 1VJ4 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:// | + | 1VJ4 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJ4 OCA]. |
==Reference== | ==Reference== | ||
Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=6854642 6854642] | Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=6854642 6854642] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Cruse, W | + | [[Category: Cruse, W B.]] |
[[Category: Kennard, O.]] | [[Category: Kennard, O.]] | ||
[[Category: Rabinovich, D.]] | [[Category: Rabinovich, D.]] | ||
| - | [[Category: Salisbury, S | + | [[Category: Salisbury, S A.]] |
[[Category: Shakked, Z.]] | [[Category: Shakked, Z.]] | ||
| - | [[Category: Viswamitra, M | + | [[Category: Viswamitra, M A.]] |
[[Category: a-dna]] | [[Category: a-dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:35:56 2008'' |
Revision as of 13:36, 21 February 2008
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SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)
Overview
The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.
About this Structure
1VJ4 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C)., Shakked Z, Rabinovich D, Kennard O, Cruse WB, Salisbury SA, Viswamitra MA, J Mol Biol. 1983 May 15;166(2):183-201. PMID:6854642
Page seeded by OCA on Thu Feb 21 15:35:56 2008
