2izm: Difference between revisions

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OCA

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-[[Image:2izm.gif|left|200px]]<br /><applet load="2izm" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2izm, resolution 2.70&Aring;" />
-'''MS2-RNA HAIRPIN (C-10) COMPLEX'''<br />
-==Overview==
+==MS2-RNA HAIRPIN (C-10) COMPLEX==
-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.
+<StructureSection load='2izm' size='340' side='right'caption='[[2izm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2izm]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_MS2 Escherichia phage MS2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kuo 1kuo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IZM FirstGlance]. <br>
-IZM is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. This structure superseeds the now removed PDB entry 1KUO. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IZM OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2izm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2izm OCA], [https://pdbe.org/2izm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2izm RCSB], [https://www.ebi.ac.uk/pdbsum/2izm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2izm ProSAT]</span></td></tr>
-==Reference==
+</table>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12060685 12060685]
+== Function ==
-[[Category: Enterobacterio phage ms2]]
+[https://www.uniprot.org/uniprot/CAPSD_BPMS2 CAPSD_BPMS2] Self-assembles to form the T=3 icosahedral virus shell that protects the viral nucleic acid. Acts as a translational repressor by binding with high specificity to a single stem-loop structure in the genomic RNA that contains the initiation codon of the gene for the viral replicase. Involved in virus assembly through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome.<ref>PMID:16531233</ref> <ref>PMID:18662904</ref> <ref>PMID:26608810</ref> <ref>PMID:8254664</ref> <ref>PMID:9245600</ref> <ref>PMID:9469847</ref>
-[[Category: Protein complex]]
+== Evolutionary Conservation ==
-[[Category: Grahn, E.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Helgstrand, C.]]
+Check<jmol>
-[[Category: Liljas, L.]]
+  <jmolCheckbox>
-[[Category: Moss, T.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iz/2izm_consurf.spt"</scriptWhenChecked>
-[[Category: Stockley, P.G.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: Stonehouse, N.J.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: Tars, K.]]
+  </jmolCheckbox>
-[[Category: capsid]]
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2izm ConSurf].
-[[Category: capsid protein]]
+<div style="clear:both"></div>
-[[Category: complex (capsid protein-rna hairpin)]]
+== References ==
-[[Category: hairpin]]
+<references/>
-[[Category: levivirus]]
+__TOC__
-[[Category: rna-binding]]
+</StructureSection>
-[[Category: structural protein]]
+[[Category: Escherichia phage MS2]]
-[[Category: virion protein]]
+[[Category: Large Structures]]
-[[Category: virus/rna complex]]
+[[Category: Grahn E]]
-[[Category: virus/viral protein/rna]]
+[[Category: Helgstrand C]]
+[[Category: Liljas L]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:29:08 2007''
+[[Category: Moss T]]
+[[Category: Stockley PG]]
+[[Category: Stonehouse NJ]]
+[[Category: Tars K]]