1zfa: Difference between revisions
New page: left|200px<br /><applet load="1zfa" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zfa, resolution 1.56Å" /> '''GGA Duplex A-DNA'''<... |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1zfa.gif|left|200px]]<br /><applet load="1zfa" size=" | [[Image:1zfa.gif|left|200px]]<br /><applet load="1zfa" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1zfa, resolution 1.56Å" /> | caption="1zfa, resolution 1.56Å" /> | ||
'''GGA Duplex A-DNA'''<br /> | '''GGA Duplex A-DNA'''<br /> | ||
==Overview== | ==Overview== | ||
The fundamental question of how sequence defines conformation is | The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects. | ||
==About this Structure== | ==About this Structure== | ||
1ZFA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NA and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | 1ZFA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFA OCA]. | ||
==Reference== | ==Reference== | ||
| Line 14: | Line 14: | ||
[[Category: Cavaliere, E.]] | [[Category: Cavaliere, E.]] | ||
[[Category: Harms, M.]] | [[Category: Harms, M.]] | ||
[[Category: Hays, F | [[Category: Hays, F A.]] | ||
[[Category: Ho, P | [[Category: Ho, P S.]] | ||
[[Category: Jones, Z | [[Category: Jones, Z J.R.]] | ||
[[Category: Raup, D.]] | [[Category: Raup, D.]] | ||
[[Category: Teegarden, A | [[Category: Teegarden, A T.]] | ||
[[Category: Watson, J.]] | [[Category: Watson, J.]] | ||
[[Category: CA]] | [[Category: CA]] | ||
| Line 27: | Line 27: | ||
[[Category: molecular structure]] | [[Category: molecular structure]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:14:57 2008'' | ||
Revision as of 17:14, 21 February 2008
|
GGA Duplex A-DNA
OverviewOverview
The fundamental question of how sequence defines conformation is explicitly answered if the structures of all possible sequences of a macromolecule are determined. We present here a crystallographic screen of all permutations of the inverted repeat DNA sequence d(CCnnnN6N7N8GG), where N6, N7, and N8 are any of the four naturally occurring nucleotides. At this point, 63 of the 64 possible permutations have been crystallized from a defined set of solutions. When combined with previous work, we have assembled a data set of 37 single-crystal structures from 29 of the sequences in this motif, representing three structural classes of DNA (B-DNA, A-DNA, and four-stranded Holliday junctions). This data set includes a unique set of amphimorphic sequence, those that crystallize in two different conformations and serve to bridge the three structural phases. We have thus constructed a map of DNA structures that can be walked through in single nucleotide steps. Finally, the resulting data set allows us to dissect in detail the stabilization of and conformational variations within structural classes and identify significant conformational deviations within a particular structural class that result from sequence rather than crystal or crystallization effects.
About this StructureAbout this Structure
1ZFA is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
ReferenceReference
How sequence defines structure: a crystallographic map of DNA structure and conformation., Hays FA, Teegarden A, Jones ZJ, Harms M, Raup D, Watson J, Cavaliere E, Ho PS, Proc Natl Acad Sci U S A. 2005 May 17;102(20):7157-62. Epub 2005 May 3. PMID:15870206
Page seeded by OCA on Thu Feb 21 16:14:57 2008