1U1Y

Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position

Summary for 1U1Y

• Entry DOI: 10.2210/pdb1u1y/pdb
• Related: 1AQ3 1AQ4 1BMS 1E6T 1E7X 1ZDS
• Descriptor: 5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3', Coat protein (3 entities in total)
• Functional Keywords: complex (capsid protein-rna hairpin), hairpin, capsid, levivirus, icosahedral virus, virus-rna complex, virus/rna
• Biological source: Enterobacterio phage MS2
• Cellular location: Virion (Potential): P03612
• Total number of polymer chains: 5
• Total formula weight: 52144.11

Authors

Horn, W.T.,Convery, M.A.,Stonehouse, N.J.,Adams, C.J.,Liljas, L.,Phillips, S.E.,Stockley, P.G. (deposition date: 2004-07-16, release date: 2004-12-07, Last modification date: 2023-08-23)

Primary citation

Horn, W.T.,Convery, M.A.,Stonehouse, N.J.,Adams, C.J.,Liljas, L.,Phillips, S.E.,Stockley, P.G.
The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions.
Rna, 10:1776-1782, 2004

PubMed Abstract: We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.

PubMed: 15496523
DOI: 10.1261/rna.7710304

Experimental method

X-RAY DIFFRACTION (2.85 Å)