2iz8: Difference between revisions

Revision as of 18:57, 21 February 2008

MS2-RNA HAIRPIN (C-7) COMPLEX

OverviewOverview

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.

About this StructureAbout this Structure

2IZ8 is a Single protein structure of sequence from Enterobacterio phage ms2. This structure supersedes the now removed PDB entry 1GKV. Full crystallographic information is available from OCA.

ReferenceReference

Investigating the structural basis of purine specificity in the structures of MS2 coat protein RNA translational operator hairpins., Helgstrand C, Grahn E, Moss T, Stonehouse NJ, Tars K, Stockley PG, Liljas L, Nucleic Acids Res. 2002 Jun 15;30(12):2678-85. PMID:12060685

Page seeded by OCA on Thu Feb 21 17:57:36 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:2iz8.gif|left|200px]]<br /><applet load="2iz8" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2iz8.gif|left|200px]]<br /><applet load="2iz8" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2iz8, resolution 3.30&Aring;" />
 '''MS2-RNA HAIRPIN (C-7) COMPLEX'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-IZ8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. This structure superseeds the now removed PDB entry 1GKV. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IZ8 OCA].
+IZ8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. This structure supersedes the now removed PDB entry 1GKV. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZ8 OCA].
 ==Reference==
@@ Line 16: / Line 16: @@
 [[Category: Helgstrand, C.]]
 [[Category: Liljas, L.]]
-[[Category: Stockley, P.G.]]
+[[Category: Stockley, P G.]]
-[[Category: Stonehouse, N.J.]]
+[[Category: Stonehouse, N J.]]
 [[Category: capsid]]
 [[Category: complex (capsid protein/rna hairpin)]]
@@ Line 24: / Line 24: @@
 [[Category: virus]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:28:17 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:57:36 2008''