9K7R

Crystal structure of DNA/RNA duplex obtained using the counter diffusion method on Earth (K form)

Summary for 9K7R

• Entry DOI: 10.2210/pdb9k7r/pdb
• Descriptor: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3'), DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3'), SPERMINE, ... (4 entities in total)
• Functional Keywords: counter diffusion method, rna-dna complex, rna/dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 5845.02

Authors

Kondo, J.,Ando, S. (deposition date: 2024-10-24, release date: 2025-02-19, Last modification date: 2025-03-12)

Primary citation

Ando, S.,Takahashi, M.,Kondo, J.
The first report of structural analysis of a nucleic acid using crystals grown in space.
Acta Crystallogr.,Sect.F, 81:95-100, 2025

PubMed Abstract: For the success of structure-based drug design, three-dimensional structures solved by X-ray crystallography at atomic resolution are mandatory. In order to obtain high-quality single crystals with strong diffraction power, crystallization under microgravity conditions has been attempted for proteins. Since nucleic acid duplexes have chemical, structural and crystallographic characteristics that differ from those of globular proteins, such as intermolecular repulsion due to negative charge and molecular and crystallographic anisotropies, it is interesting to investigate whether microgravity crystallization improves the crystal growth of nucleic acids. However, to our knowledge there has been only one report on nucleic acid crystallization in a microgravity environment, and there have been no reports of successful structural analysis. Here, we conducted the crystallization of a DNA/RNA heteroduplex in space. The heteroduplex was successfully crystallized in a microgravity environment, and the size and appearance of the crystals were improved compared with control experiments conducted on Earth. Although the effect of the counter-diffusion method is likely to be more significant than the effect of microgravity in this study, we were able to analyze the structure at a higher resolution (1.4 Å) than our previously reported crystal structure (1.9 Å).

PubMed: 39937045
DOI: 10.1107/S2053230X25000810

Experimental method

X-RAY DIFFRACTION (1.59 Å)