100D

CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING

Summary for 100D

• Entry DOI: 10.2210/pdb100d/pdb
• Descriptor: DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3'), SPERMINE (3 entities in total)
• Functional Keywords: a-dna/rna, double helix, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 6360.30

Authors

Ban, C.,Ramakrishnan, B.,Sundaralingam, M. (deposition date: 1994-12-05, release date: 1995-03-31, Last modification date: 2023-11-22)

Primary citation

Ban, C.,Ramakrishnan, B.,Sundaralingam, M.
Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing.
Nucleic Acids Res., 22:5466-5476, 1994

PubMed Abstract: The crystal structure of the self-complementary chimeric decamer duplex r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved at 1.9 A resolution by the molecular replacement method and refined to an R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the terminal riboses apparently drive the entire chimeric duplex into an A-DNA conformation, in contrast to the B-DNA conformation adopted by the all-deoxy decamer of the same sequence. Five symmetry related duplexes encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and hydrogen bonding interactions. The spermine interaction severely bends the duplexes by 31 degrees into the major groove at the fourth base pair G(4).C(17), jolts it and slides the 'base plate' into the minor groove. This base pair, together with the adjacent base pair in the top half and the corresponding pseudo two-fold related base pairs in the bottom half, form four minor groove base-paired multiples with the terminal base pairs of two neighboring duplexes.

PubMed: 7816639
DOI: 10.1093/nar/22.24.5466

Experimental method

X-RAY DIFFRACTION (1.9 Å)