1zdi

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[[Image:1zdi.gif|left|200px]]
 
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==RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX==
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The line below this paragraph, containing "STRUCTURE_1zdi", creates the "Structure Box" on the page.
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<StructureSection load='1zdi' size='340' side='right'caption='[[1zdi]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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</table>
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{{STRUCTURE_1zdi| PDB=1zdi | SCENE= }}
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== Function ==
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[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>
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'''RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX'''
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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==Overview==
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/1zdi_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1zdi ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== 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.
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.
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==About this Structure==
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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>
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1ZDI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDI OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://www.ncbi.nlm.nih.gov/pubmed/9245600 9245600]
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</div>
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[[Category: Enterobacterio phage ms2]]
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<div class="pdbe-citations 1zdi" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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== References ==
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[[Category: K Valegard]]
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<references/>
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[[Category: L Liljas]]
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__TOC__
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[[Category: Worm, S Van Den.]]
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</StructureSection>
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[[Category: Coat protein]]
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[[Category: Escherichia phage MS2]]
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[[Category: Icosahedral virus]]
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[[Category: Large Structures]]
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[[Category: Rna fragment]]
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[[Category: Liljas L]]
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[[Category: Rna-binding]]
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[[Category: Valegard K]]
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[[Category: Viral protein capsid]]
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[[Category: Van Den Worm S]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:29:44 2008''
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Current revision

RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX

PDB ID 1zdi

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