1sk5: Difference between revisions

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[[Image:1sk5.gif|left|200px]]
[[Image:1sk5.png|left|200px]]


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{{STRUCTURE_1sk5|  PDB=1sk5  |  SCENE=  }}  
{{STRUCTURE_1sk5|  PDB=1sk5  |  SCENE=  }}  


'''The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition'''
===The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition===




==Overview==
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For the first time, ab initio direct methods have been used to solve the crystal structure of an RNA/DNA hybrid decamer. The RNA/DNA sequence corresponds to the leftmost two-thirds of the polypurine tract (PPT), the primer for second-strand DNA synthesis by HIV-1 reverse transcriptase (RT). Direct methods using Shake-and-Bake (SnB) yielded solutions for the RNA/DNA decamer molecule using 1.15 A data, which is just on the resolution edge of what might work with direct methods. Atomic positions for 96% of the entire molecule, containing 514 non-H atoms including three Ca(2+) ions, were easily interpreted from a Fourier map based on the 'Shake-and-Bake' minimal function and CROQUE phase-refinement program. Only six atoms, primarily in the sugar linkage, were missing in this Fourier map. At present, the R factor of the model is 0.143 (R(free) = 0.186) for the 562 non-H atom sites located. The conformation of the RNA/DNA helix is A-form, with a typical A-helix minor-groove width. This paper presents the methodology used in solving this structure.
The line below this paragraph, {{ABSTRACT_PUBMED_11173466}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 11173466 is the PubMed ID number.
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{{ABSTRACT_PUBMED_11173466}}


==About this Structure==
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA].  
[[1sk5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SK5 OCA].  


==Reference==
==Reference==
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution., Han GW, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173466 11173466]
<ref group="xtra">PMID:11173466</ref><ref group="xtra">PMID:14636594</ref><ref group="xtra">PMID:9223643</ref><references group="xtra"/>
[[Category: Dickerson, R E.]]
[[Category: Dickerson, R E.]]
[[Category: Han, G W.]]
[[Category: Han, G W.]]
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[[Category: Dna/dna double helix]]
[[Category: Dna/dna double helix]]
[[Category: Popypurine tract sequence of hiv-1]]
[[Category: Popypurine tract sequence of hiv-1]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:48:20 2008''

Revision as of 22:02, 14 March 2011

File:1sk5.png

Template:STRUCTURE 1sk5

The ultra-high resolution structure of d(CTTTTAAAAG)2: modulation of bending by T-A steps and its role in DNA recognition

Template:ABSTRACT PUBMED 11173466

About this Structure

1sk5 is a 2 chain structure. Full crystallographic information is available from OCA.

Reference

  1. Han GW. Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 A resolution. Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):213-8. PMID:11173466
  2. Kopka ML, Lavelle L, Han GW, Ng HL, Dickerson RE. An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H. J Mol Biol. 2003 Dec 5;334(4):653-65. PMID:14636594
  3. Han GW, Kopka ML, Cascio D, Grzeskowiak K, Dickerson RE. Structure of a DNA analog of the primer for HIV-1 RT second strand synthesis. J Mol Biol. 1997 Jun 27;269(5):811-26. PMID:9223643 doi:S0022-2836(97)91085-8

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