This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2bu1
From Proteopedia
(Difference between revisions)
| (6 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| + | |||
==MS2-RNA HAIRPIN (5BRU -5) COMPLEX== | ==MS2-RNA HAIRPIN (5BRU -5) COMPLEX== | ||
| - | <StructureSection load='2bu1' size='340' side='right' caption='[[2bu1]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='2bu1' size='340' side='right'caption='[[2bu1]], [[Resolution|resolution]] 2.20Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2bu1]] is a 5 chain structure with sequence from [ | + | <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> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[ | + | <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> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <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> |
| - | <table> | + | </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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bu/2bu1_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bu/2bu1_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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]. |
<div style="clear:both"></div> | <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. | ||
| - | |||
| - | 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> | ||
| - | + | ==See Also== | |
| - | + | *[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] | |
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Escherichia phage MS2]] |
| - | [[Category: Davis | + | [[Category: Large Structures]] |
| - | [[Category: Fridborg | + | [[Category: Davis DR]] |
| - | [[Category: Grahn | + | [[Category: Fridborg K]] |
| - | [[Category: Helgstrand | + | [[Category: Grahn E]] |
| - | [[Category: Lago | + | [[Category: Helgstrand C]] |
| - | [[Category: Liljas | + | [[Category: Lago H]] |
| - | [[Category: Moss | + | [[Category: Liljas L]] |
| - | [[Category: Stockley | + | [[Category: Moss T]] |
| - | [[Category: Stonehouse | + | [[Category: Stockley PG]] |
| - | [[Category: Sundaram | + | [[Category: Stonehouse NJ]] |
| - | [[Category: Tars | + | [[Category: Sundaram M]] |
| - | + | [[Category: Tars K]] | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
MS2-RNA HAIRPIN (5BRU -5) COMPLEX
| |||||||||||
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
