1EFO

CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)

Summary for 1EFO

• Entry DOI: 10.2210/pdb1efo/pdb
• Descriptor: DNA (5'-D(*CP*TP*CP*CP*TP*CP*TP*TP*C)-3'), RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3') (3 entities in total)
• Functional Keywords: a-form conformation, hybrid, adenine bulge, looped out, dna-rna complex, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 5944.82

Authors

Sudarsanakumar, C.,Xiong, Y.,Sundaralingam, M. (deposition date: 2000-02-09, release date: 2000-05-29, Last modification date: 2024-02-07)

Primary citation

Sudarsanakumar, C.,Xiong, Y.,Sundaralingam, M.
Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag).
J.Mol.Biol., 299:103-112, 2000

PubMed Abstract: Crystal structure of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag), with an adenine bulge in the polypurine RNA strand was determined at 2.3 A resolution. The structure was solved by the molecular replacement method and refined to a final R-factor of 19.9% (Rfree 22.2%). The hybrid duplex crystallized in the space group I222 with unit cell dimensions, a = 46.66 A, b = 47.61 A and c = 54.05 A, and adopts the A-form conformation. All RNA and DNA sugars are in the C3'-endo conformation, the glycosyl angles in anti conformation and the majority of the C4'-C5' torsion angles in g+ except two trans angles, in conformity with the C3'-endo rigid nucleotide hypothesis. The adenine bulge is looped out and it is also in the anti C3'-endo conformation. The bulge is involved in a base-triple (C.g)*a interaction with the end base-pair (C9.g10) in the minor groove of a symmetry-related molecule. The 2' hydroxyl group of g15 is hydrogen bonded to O2P and O5' of g17, skipping the bulged adenine a16 and stabilizing the sugar-phosphate backbone of the hybrid. The hydrogen bonding and the backbone conformation at the bulged adenine site is very similar to that found in the crystal structure of a protein-RNA complex.

PubMed: 10860725
DOI: 10.1006/jmbi.2000.3730

Experimental method

X-RAY DIFFRACTION (2.3 Å)