2bu1

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[[Image:2bu1.gif|left|200px]]
 
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==MS2-RNA HAIRPIN (5BRU -5) COMPLEX==
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The line below this paragraph, containing "STRUCTURE_2bu1", creates the "Structure Box" on the page.
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<StructureSection load='2bu1' size='340' side='right'caption='[[2bu1]], [[Resolution|resolution]] 2.20&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'>[[2bu1]] 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=1e6t 1e6t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BU1 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
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{{STRUCTURE_2bu1| PDB=2bu1 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bu1 OCA], [https://pdbe.org/2bu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bu1 RCSB], [https://www.ebi.ac.uk/pdbsum/2bu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bu1 ProSAT]</span></td></tr>
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</table>
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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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== 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/bu/2bu1_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=2bu1 ConSurf].
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<div style="clear:both"></div>
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'''MS2-RNA HAIRPIN (5BRU-5) COMPLEX'''
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==See Also==
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*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
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== References ==
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==Overview==
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<references/>
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We have determined the X-ray structures of six MS2 RNA hairpin-coat-protein complexes having five different substitutions at the hairpin loop base -5. This is a uracil in the wild-type hairpin and contacts the coat protein both by stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine side chain. The RNA consensus sequence derived from coat protein binding studies with natural sequence variants suggested that the -5 base needs to be a pyrimidine for strong binding. The five -5 substituents used in this study were 5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The structure of the 5-bromouracil complex was determined to 2.2 A resolution, which is the highest to date for any MS2 RNA-protein complex. All the complexes presented here show very similar conformations, despite variation in affinity in solution. The results suggest that the stacking of the -5 base on to the tyrosine side chain is the most important driving force for complex formation. A number of hydrogen bonds that are present in the wild-type complex are not crucial for binding, as they are missing in one or more of the complexes. The results also reveal the flexibility of this RNA-protein interface, with respect to functional group variation, and may be generally applicable to other RNA-protein complexes.
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia phage MS2]]
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2BU1 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1e6t 1e6t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BU1 OCA].
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[[Category: Large Structures]]
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[[Category: Davis DR]]
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==Reference==
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[[Category: Fridborg K]]
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Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex., Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L, RNA. 2001 Nov;7(11):1616-27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11720290 11720290]
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[[Category: Grahn E]]
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[[Category: Enterobacterio phage ms2]]
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[[Category: Helgstrand C]]
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[[Category: Protein complex]]
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[[Category: Lago H]]
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[[Category: Davis, D.]]
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[[Category: Liljas L]]
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[[Category: Fridborg, K.]]
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[[Category: Moss T]]
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[[Category: Grahn, E.]]
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[[Category: Stockley PG]]
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[[Category: Helgstrand, C.]]
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[[Category: Stonehouse NJ]]
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[[Category: Lago, H.]]
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[[Category: Sundaram M]]
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[[Category: Liljas, L.]]
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[[Category: Tars K]]
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[[Category: Moss, T.]]
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[[Category: Stockley, P.]]
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[[Category: Stonehouse, N.]]
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[[Category: Sundaram, M.]]
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[[Category: Tars, K.]]
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[[Category: Capsid]]
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[[Category: Capsid protein]]
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[[Category: Hairpin]]
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[[Category: Icosahedral virus]]
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[[Category: Levivirus]]
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[[Category: Rna-binding]]
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[[Category: Structural protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 20:47:51 2008''
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Current revision

MS2-RNA HAIRPIN (5BRU -5) COMPLEX

PDB ID 2bu1

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