2IZM

MS2-RNA HAIRPIN (C-10) COMPLEX

Replaces:  1KUO

Summary for 2IZM

• Entry DOI: 10.2210/pdb2izm/pdb
• Related: 1AQ3 1AQ4 1BMS 1MSC 1MST 1MVA 1MVB 1U1Y 1ZDH 1ZDI 1ZDJ 1ZDK 1ZSE 2B2D 2B2E 2B2G 2BNY 2BQ5 2BS0 2BS1 2BU1 2C4Q 2C4Y 2C4Z 2C50 2C51 2IZ8 2IZ9 2IZN 2MS2 5MSF 6MSF 7MSF
• Descriptor: Capsid protein, 5'-R(*AP*CP*AP*UP*GP*CP*GP*GP*AP*UP *CP*AP*CP*CP*CP*AP*UP*GP*U)-3' (3 entities in total)
• Functional Keywords: virus/rna, virus/viral protein/rna, complex (capsid protein-rna hairpin), virion protein, capsid protein, structural protein, capsid, hairpin, levivirus, rna-binding, virus-rna complex
• Biological source: Escherichia phage MS2; More
• Cellular location: Virion : C0M1L4
• Total number of polymer chains: 5
• Total formula weight: 53290.69

Authors

Helgstrand, C.,Grahn, E.,Moss, T.,Stonehouse, N.J.,Tars, K.,Stockley, P.G.,Liljas, L. (deposition date: 2006-07-25, release date: 2007-07-03, Last modification date: 2024-03-06)

Primary citation

Helgstrand, C.,Grahn, E.,Moss, T.,Stonehouse, N.J.,Tars, K.,Stockley, P.G.,Liljas, L.
Investigating the Structural Basis of Purine Specificity in the Structures of MS2 Coat Protein RNA Translational Operator Complexes
Nucleic Acids Res., 30:2678-, 2002

PubMed Abstract: We have determined the structures of complexes between the phage MS2 coat protein and variants of the replicase translational operator in order to explore the sequence specificity of the RNA-protein interaction. The 19-nt RNA hairpins studied have substitutions at two positions that have been shown to be important for specific binding. At one of these positions, -10, which is a bulged adenosine (A) in the stem of the wild-type operator hairpin, substitutions were made with guanosine (G), cytidine (C) and two non-native bases, 2-aminopurine (2AP) and inosine (I). At the other position, -7 in the hairpin loop, the native adenine was substituted with a cytidine. Of these, only the G-10, C-10 and C-7 variants showed interpretable density for the RNA hairpin. In spite of large differences in binding affinities, the structures of the variant complexes are very similar to the wild-type operator complex. For G-10 substitutions in hairpin variants that can form bulges at alternative places in the stem, the binding affinity is low and a partly disordered conformation is seen in the electron density maps. The affinity is similar to that of wild-type when the base pairs adjacent to the bulged nucleotide are selected to avoid alternative conformations. Both purines bind in a very similar way in a pocket in the protein. In the C-10 variant, which has very low affinity, the cytidine is partly inserted in the protein pocket rather than intercalated in the RNA stem. Substitution of the wild-type adenosine at position -7 by pyrimidines gives strongly reduced affinities, but the structure of the C-7 complex shows that the base occupies the same position as the A-7 in the wild-type RNA. It is stacked in the RNA and makes no direct contact with the protein.

PubMed: 12060685
DOI: 10.1093/NAR/GKF371

Experimental method

X-RAY DIFFRACTION (2.7 Å)