1ybn
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1ybn |SIZE=350|CAPTION= <scene name='initialview01'>1ybn</scene> | |PDB= 1ybn |SIZE=350|CAPTION= <scene name='initialview01'>1ybn</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[294d|294D]], [[1ybl|1YBL]], [[1ybr|1YBR]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ybn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ybn OCA], [http://www.ebi.ac.uk/pdbsum/1ybn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ybn RCSB]</span> | ||
}} | }} | ||
| Line 23: | Line 26: | ||
[[Category: Esmaili, N.]] | [[Category: Esmaili, N.]] | ||
[[Category: Leroy, J L.]] | [[Category: Leroy, J L.]] | ||
| - | [[Category: dna | + | [[Category: dna]] |
| + | [[Category: hemiprotonated cytidine]] | ||
| + | [[Category: i-motif]] | ||
| + | [[Category: telomer]] | ||
| + | [[Category: tetrahymena]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:02:01 2008'' |
Revision as of 22:02, 30 March 2008
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| Ligands: | , | ||||||
| Related: | 294D, 1YBL, 1YBR
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Solution structure of the 3'E topology of the i-motif tetramer of d(CCCCAA)
Overview
Using NMR methods, we have resolved the i-motif structures formed by d(AACCCC) and by d(CCCCAA), two versions of the DNA sequence repeated in the telomeric regions of the C-rich strand of tetrahymena chromosomes. Both oligonucleotides form fully symmetrical i-motif tetramers built by intercalation of two hemiprotonated duplexes containing four C*C+ pairs. The structures are extremely stable. In the tetramer of d(AACCCC), the outermost C*C+ pairs are formed by the cytidines of the 5' ends of the cytidine tracts. A2 forms an A2*A2 (H6trans-N7) pair stacked to C3*C3+ and cross-strand stacked to A1. At 0 degrees C, the lifetimes of the hemiprotonated pairs range from 1 ms for the outermost pair to approximately 1 h for the innermost pairs. The tetramer of d(CCCCAA) adopts two distinct intercalation topologies in slow conformational exchange. One, whose outermost C*C+ pairs are built by the cytidines of the 5' end and the other by those of the 3' end. In both topologies, the adenosine bases are fairly well stacked to the adjacent C*C+ pairs. They are not paired but form symmetrical pseudo-pairs with their H6cis amino proton and N1 nitrogen pointing towards each other.
About this Structure
1YBN is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats., Esmaili N, Leroy JL, Nucleic Acids Res. 2005 Jan 12;33(1):213-24. Print 2005. PMID:15647504
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