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New page: left|200px<br /><applet load="1zdi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zdi, resolution 2.700Å" /> '''RNA BACTERIOPHAGE M...
 
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[[Image:1zdi.gif|left|200px]]<br /><applet load="1zdi" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1zdi, resolution 2.700&Aring;" />
'''RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX'''<br />


==Overview==
==RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX==
Crystal structures of two complexes between recombinant MS2 capsids and, RNA operator fragments have been determined at 2.7 A resolution. The coat, protein of the RNA bacteriophage MS2 is bifunctional; it forms the, icosahedral virus shell to protect the viral nucleic acid and it acts as a, translational repressor by binding with high specificity to a unique site, on the RNA, a single stem-loop structure, containing the initiation codon, of the gene for the viral replicase. In order to determine the structure, of these protein-RNA complexes, we have used chemically synthesized, variants of the stem-loop fragment and soaked them into crystals of, recombinant capsids. The RNA stem-loop, as bound to the protein, forms a, crescent-like structure and interacts with the surface of the beta-sheet, of a coat protein dimer. It makes protein contacts with seven phosphate, groups on the 5' side of the stem-loop, with a pyrimidine base at position, -5, which stacks onto a tyrosine, and with two exposed adenine bases, one, in the loop and one at a bulge in the stem. Replacement of the wild-type, uridine with a cytosine at position -5 increases the affinity of the RNA, to the dimer significantly. The complex with RNA stem-loop having cytosine, at this position differs from that of the wild-type complex mainly by, having one extra intramolecular RNA interaction and one extra, water-mediated hydrogen bond.
<StructureSection load='1zdi' size='340' side='right'caption='[[1zdi]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1zdi]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_MS2 Escherichia phage MS2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZDI FirstGlance]. <br>
</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=1zdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zdi OCA], [https://pdbe.org/1zdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zdi RCSB], [https://www.ebi.ac.uk/pdbsum/1zdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zdi ProSAT]</span></td></tr>
</table>
== Function ==
[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 ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/1zdi_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1zdi ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by binding with high specificity to a unique site on the RNA, a single stem-loop structure, containing the initiation codon of the gene for the viral replicase. In order to determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with the surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 5' side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, and with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at position -5 increases the affinity of the RNA to the dimer significantly. The complex with RNA stem-loop having cytosine at this position differs from that of the wild-type complex mainly by having one extra intramolecular RNA interaction and one extra water-mediated hydrogen bond.


==About this Structure==
The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.,Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:9245600<ref>PMID:9245600</ref>
1ZDI 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]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ZDI OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions., Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L, J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9245600 9245600]
</div>
[[Category: Enterobacterio phage ms2]]
<div class="pdbe-citations 1zdi" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
== References ==
[[Category: K.Valegard]]
<references/>
[[Category: L.Liljas]]
__TOC__
[[Category: Worm, S.Van.Den.]]
</StructureSection>
[[Category: coat protein]]
[[Category: Escherichia phage MS2]]
[[Category: complex (coat protein/rna)]]
[[Category: Large Structures]]
[[Category: icosahedral virus]]
[[Category: Liljas L]]
[[Category: rna fragment]]
[[Category: Valegard K]]
[[Category: rna-binding]]
[[Category: Van Den Worm S]]
[[Category: viral protein capsid]]
 
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