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==MS2-RNA HAIRPIN (C-10) COMPLEX==
==MS2-RNA HAIRPIN (C-10) COMPLEX==
<StructureSection load='2izm' size='340' side='right' caption='[[2izm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='2izm' size='340' side='right'caption='[[2izm]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2izm]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_ms2 Bacteriophage 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IZM FirstGlance]. <br>
<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>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1aq3|1aq3]], [[1aq4|1aq4]], [[1bms|1bms]], [[1msc|1msc]], [[1mst|1mst]], [[1mva|1mva]], [[1mvb|1mvb]], [[1u1y|1u1y]], [[1zdh|1zdh]], [[1zdi|1zdi]], [[1zdj|1zdj]], [[1zdk|1zdk]], [[1zse|1zse]], [[2b2d|2b2d]], [[2b2e|2b2e]], [[2b2g|2b2g]], [[2bny|2bny]], [[2bq5|2bq5]], [[2bs0|2bs0]], [[2bs1|2bs1]], [[2bu1|2bu1]], [[2c4q|2c4q]], [[2c4y|2c4y]], [[2c4z|2c4z]], [[2c50|2c50]], [[2c51|2c51]], [[2ms2|2ms2]], [[5msf|5msf]], [[6msf|6msf]], [[7msf|7msf]], [[2iz8|2iz8]], [[2iz9|2iz9]], [[2izn|2izn]]</td></tr>
</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2izm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2izm OCA], [http://pdbe.org/2izm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2izm RCSB], [http://www.ebi.ac.uk/pdbsum/2izm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2izm ProSAT]</span></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>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/COAT_BPMS2 COAT_BPMS2]] Forms the phage shell; binds to the phage RNA.  
[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:12060685</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2izm" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteriophage ms2]]
[[Category: Escherichia phage MS2]]
[[Category: Grahn, E]]
[[Category: Large Structures]]
[[Category: Helgstrand, C]]
[[Category: Grahn E]]
[[Category: Liljas, L]]
[[Category: Helgstrand C]]
[[Category: Moss, T]]
[[Category: Liljas L]]
[[Category: Stockley, P G]]
[[Category: Moss T]]
[[Category: Stonehouse, N J]]
[[Category: Stockley PG]]
[[Category: Tars, K]]
[[Category: Stonehouse NJ]]
[[Category: Capsid]]
[[Category: Tars K]]
[[Category: Capsid protein]]
[[Category: Hairpin]]
[[Category: Levivirus]]
[[Category: Rna-binding]]
[[Category: Structural protein]]
[[Category: Virion protein]]
[[Category: Virus-rna complex]]
[[Category: Virus/rna]]
[[Category: Virus/viral protein/rna]]
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