1u1y

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[[Image:1u1y.png|left|200px]]
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==Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position==
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<StructureSection load='1u1y' size='340' side='right' caption='[[1u1y]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1u1y]] is a 5 chain structure with 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=1U1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U1Y FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PR:2-AMINO-9-[2-DEOXYRIBOFURANOSYL]-9H-PURINE-5-MONOPHOSPHATE'>2PR</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1aq3|1aq3]], [[1aq4|1aq4]], [[1bms|1bms]], [[1zds|1zds]], [[1e6t|1e6t]], [[1e7x|1e7x]]</td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1u1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u1y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u1y RCSB], [http://www.ebi.ac.uk/pdbsum/1u1y PDBsum]</span></td></tr>
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<table>
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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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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u1/1u1y_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/chain_selection.php?pdb_ID=2ata 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 ==
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We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.
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{{STRUCTURE_1u1y| PDB=1u1y | SCENE= }}
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The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions.,Horn WT, Convery MA, Stonehouse NJ, Adams CJ, Liljas L, Phillips SE, Stockley PG RNA. 2004 Nov;10(11):1776-82. PMID:15496523<ref>PMID:15496523</ref>
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===Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_15496523}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[1u1y]] is a 5 chain structure with 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=1U1Y OCA].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:015496523</ref><references group="xtra"/>
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[[Category: Enterobacterio phage ms2]]
[[Category: Enterobacterio phage ms2]]
[[Category: Adams, C J.]]
[[Category: Adams, C J.]]

Revision as of 09:45, 3 October 2014

Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position

1u1y, resolution 2.85Å

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