2c51: Difference between revisions

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{{Seed}}
[[Image:2c51.png|left|200px]]


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==MS2-RNA HAIRPIN (G -5) COMPLEX==
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<StructureSection load='2c51' size='340' side='right'caption='[[2c51]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2c51]] 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=1h8j 1h8j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C51 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C51 FirstGlance]. <br>
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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]] 2.8&#8491;</td></tr>
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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=2c51 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c51 OCA], [https://pdbe.org/2c51 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c51 RCSB], [https://www.ebi.ac.uk/pdbsum/2c51 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c51 ProSAT]</span></td></tr>
{{STRUCTURE_2c51|  PDB=2c51  |  SCENE=  }}
</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/c5/2c51_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=2c51 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.


===MS2-RNA HAIRPIN (G-5) COMPLEX===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
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<references/>
{{ABSTRACT_PUBMED_11720290}}
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</StructureSection>
==About this Structure==
[[Category: Escherichia phage MS2]]
2C51 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=1h8j 1h8j]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C51 OCA].
[[Category: Large Structures]]
 
[[Category: Davis DR]]
==Reference==
[[Category: Fridborg K]]
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]
[[Category: Grahn E]]
[[Category: Enterobacterio phage ms2]]
[[Category: Helgstrand C]]
[[Category: Protein complex]]
[[Category: Lago H]]
[[Category: Davis, D.]]
[[Category: Liljas L]]
[[Category: Fridborg, K.]]
[[Category: Moss T]]
[[Category: Grahn, E.]]
[[Category: Stockley PG]]
[[Category: Helgstrand, C.]]
[[Category: Stonehouse NJ]]
[[Category: Lago, H.]]
[[Category: Sundaram M]]
[[Category: Liljas, L.]]
[[Category: Tars K]]
[[Category: Moss, T.]]
[[Category: Stockley, P.]]
[[Category: Stonehouse, N.]]
[[Category: Sundaram, M.]]
[[Category: Tars, K.]]
[[Category: Capsid]]
[[Category: Hairpin]]
[[Category: Icosahedral virus]]
[[Category: Levivirus]]
[[Category: Virus coat protein]]
[[Category: Virus/viral protein/rna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:42:08 2008''

Latest revision as of 17:06, 13 December 2023

MS2-RNA HAIRPIN (G -5) COMPLEXMS2-RNA HAIRPIN (G -5) COMPLEX

Structural highlights

2c51 is a 5 chain structure with sequence from Escherichia phage MS2. This structure supersedes the now removed PDB entry 1h8j. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] [3] [4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SE, Stonehouse NJ, Liljas L, Stockley PG. Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2. Structure. 2006 Mar;14(3):487-95. PMID:16531233 doi:http://dx.doi.org/10.1016/j.str.2005.12.006
  2. ↑ Plevka P, Tars K, Liljas L. Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles. Protein Sci. 2008 Oct;17(10):1731-9. Epub 2008 Jul 28. PMID:18662904 doi:10.1110/ps.036905.108
  3. ↑ Rolfsson O, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol. 2016 Jan 29;428(2 Pt B):431-48. doi: 10.1016/j.jmb.2015.11.014. Epub , 2015 Dec 1. PMID:26608810 doi:http://dx.doi.org/10.1016/j.jmb.2015.11.014
  4. ↑ Golmohammadi R, Valegard K, Fridborg K, Liljas L. The refined structure of bacteriophage MS2 at 2.8 A resolution. J Mol Biol. 1993 Dec 5;234(3):620-39. PMID:8254664 doi:http://dx.doi.org/10.1006/jmbi.1993.1616
  5. ↑ Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:9245600 doi:http://dx.doi.org/10.1006/jmbi.1997.1144
  6. ↑ van den Worm SH, Stonehouse NJ, Valegard K, Murray JB, Walton C, Fridborg K, Stockley PG, Liljas L. Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments. Nucleic Acids Res. 1998 Mar 1;26(5):1345-51. PMID:9469847
  7. ↑ Grahn E, Moss T, Helgstrand C, Fridborg K, Sundaram M, Tars K, Lago H, Stonehouse NJ, Davis DR, Stockley PG, Liljas L. Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex. RNA. 2001 Nov;7(11):1616-27. PMID:11720290

2c51, resolution 2.80Å

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