2c4z
From Proteopedia
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| - | [[Image:2c4z.gif|left|200px]] | ||
| - | + | ==MS2-RNA HAIRPIN (2SU -5-6) COMPLEX== | |
| - | + | <StructureSection load='2c4z' size='340' side='right'caption='[[2c4z]], [[Resolution|resolution]] 2.60Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[2c4z]] 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=1hdw 1hdw]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C4Z FirstGlance]. <br> | |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> | |
| - | --> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SUR:1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5-PHOSPHATE'>SUR</scene></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=2c4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c4z OCA], [https://pdbe.org/2c4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c4z RCSB], [https://www.ebi.ac.uk/pdbsum/2c4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c4z 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/c4/2c4z_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=2c4z ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
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. | 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. | ||
| - | + | 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:11720290<ref>PMID:11720290</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 2c4z" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Davis | + | <references/> |
| - | [[Category: Fridborg | + | __TOC__ |
| - | [[Category: Grahn | + | </StructureSection> |
| - | [[Category: Helgstrand | + | [[Category: Escherichia phage MS2]] |
| - | [[Category: Lago | + | [[Category: Large Structures]] |
| - | [[Category: Liljas | + | [[Category: Davis DR]] |
| - | [[Category: Moss | + | [[Category: Fridborg K]] |
| - | [[Category: Stockley | + | [[Category: Grahn E]] |
| - | [[Category: Stonehouse | + | [[Category: Helgstrand C]] |
| - | [[Category: Sundaram | + | [[Category: Lago H]] |
| - | [[Category: Tars | + | [[Category: Liljas L]] |
| - | + | [[Category: Moss T]] | |
| - | + | [[Category: Stockley PG]] | |
| - | + | [[Category: Stonehouse NJ]] | |
| - | + | [[Category: Sundaram M]] | |
| - | + | [[Category: Tars K]] | |
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Current revision
MS2-RNA HAIRPIN (2SU -5-6) COMPLEX
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Categories: Escherichia phage MS2 | Large Structures | Davis DR | Fridborg K | Grahn E | Helgstrand C | Lago H | Liljas L | Moss T | Stockley PG | Stonehouse NJ | Sundaram M | Tars K
