2C4Y

MS2-RNA HAIRPIN (2THIOURACIL-5) COMPLEX

Replaces:  1HE0

Summary for 2C4Y

• Entry DOI: 10.2210/pdb2c4y/pdb
• Related: 1AQ3 1AQ4 1BMS 1DZS 1GKV 1GKW 1H8J 1HDW 1HE6 1KUO 1MSC 1MST 1MVA 1MVB 1U1Y 1ZDH 1ZDI 1ZDJ 1ZDK 2BNY 2BQ5 2BS0 2BS1 2BU1 2C4Z 2C50 2C51 2MS2 5MSF 6MSF 7MSF
• Descriptor: Capsid protein, 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP *SUR*AP*CP*CP*CP*AP*UP*GP*U)-3' (3 entities in total)
• Functional Keywords: virus/rna, capsid, complex (capsid protein-rna hairpin), hairpin, levivirus, virus/viral protein/rna, virus coat protein, rna- binding, icosahedral virus, virus-rna complex
• Biological source: Escherichia phage MS2; More
• Total number of polymer chains: 5
• Total formula weight: 53372.84

Authors

Grahn, E.,Moss, T.,Helgstrand, C.,Fridborg, K.,Sundaram, M.,Tars, K.,Lago, H.,Stonehouse, N.J.,Davis, D.R.,Stockley, P.G.,Liljas, L. (deposition date: 2005-10-25, release date: 2006-01-05, Last modification date: 2023-12-13)

Primary citation

Grahn, E.,Moss, T.,Helgstrand, C.,Fridborg, K.,Sundaram, M.,Tars, K.,Lago, H.,Stonehouse, N.J.,Davis, D.R.,Stockley, P.G.,Liljas, L.
Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.
Rna, 7:1616-1627, 2001

PubMed Abstract: We have determined the X-ray structures of six MS2 RNA hairpin-coat-protein complexes having five different substitutions at the hairpin loop base -5. This is a uracil in the wild-type hairpin and contacts the coat protein both by stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine side chain. The RNA consensus sequence derived from coat protein binding studies with natural sequence variants suggested that the -5 base needs to be a pyrimidine for strong binding. The five -5 substituents used in this study were 5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The structure of the 5-bromouracil complex was determined to 2.2 A resolution, which is the highest to date for any MS2 RNA-protein complex. All the complexes presented here show very similar conformations, despite variation in affinity in solution. The results suggest that the stacking of the -5 base on to the tyrosine side chain is the most important driving force for complex formation. A number of hydrogen bonds that are present in the wild-type complex are not crucial for binding, as they are missing in one or more of the complexes. The results also reveal the flexibility of this RNA-protein interface, with respect to functional group variation, and may be generally applicable to other RNA-protein complexes.

PubMed: 11720290

Experimental method

X-RAY DIFFRACTION (2.68 Å)