2iz8: Difference between revisions

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New page: left|200px<br /><applet load="2iz8" size="450" color="white" frame="true" align="right" spinBox="true" caption="2iz8, resolution 3.30Å" /> '''MS2-RNA HAIRPIN (C-7...
 
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[[Image:2iz8.gif|left|200px]]<br /><applet load="2iz8" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2iz8, resolution 3.30&Aring;" />
'''MS2-RNA HAIRPIN (C-7) COMPLEX'''<br />


==Overview==
==MS2-RNA HAIRPIN (C-7) COMPLEX==
We have determined the structures of complexes between the phage MS2 coat, protein and variants of the replicase translational operator in order to, explore the sequence specificity of the RNA-protein interaction. The 19-nt, RNA hairpins studied have substitutions at two positions that have been, shown to be important for specific binding. At one of these positions, -10, which is a bulged adenosine (A) in the stem of the wild-type operator, hairpin, substitutions were made with guanosine (G), cytidine (C) and two, non-native bases, 2-aminopurine (2AP) and inosine (I). At the other, position, -7 in the hairpin loop, the native adenine was substituted with, a cytidine. Of these, only the G-10, C-10 and C-7 variants showed, interpretable density for the RNA hairpin. In spite of large differences, in binding affinities, the structures of the variant complexes are very, similar to the wild-type operator complex. For G-10 substitutions in, hairpin variants that can form bulges at alternative places in the stem, the binding affinity is low and a partly disordered conformation is seen, in the electron density maps. The affinity is similar to that of wild-type, when the base pairs adjacent to the bulged nucleotide are selected to, avoid alternative conformations. Both purines bind in a very similar way, in a pocket in the protein. In the C-10 variant, which has very low, affinity, the cytidine is partly inserted in the protein pocket rather, than intercalated in the RNA stem. Substitution of the wild-type adenosine, at position -7 by pyrimidines gives strongly reduced affinities, but the, structure of the C-7 complex shows that the base occupies the same, position as the A-7 in the wild-type RNA. It is stacked in the RNA and, makes no direct contact with the protein.
<StructureSection load='2iz8' size='340' side='right'caption='[[2iz8]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2iz8]] 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=1gkv 1gkv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IZ8 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]] 3.3&#8491;</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=2iz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iz8 OCA], [https://pdbe.org/2iz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iz8 RCSB], [https://www.ebi.ac.uk/pdbsum/2iz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iz8 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/iz/2iz8_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=2iz8 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2IZ8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. This structure superseeds the now removed PDB entry 1GKV. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IZ8 OCA].
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 
== References ==
==Reference==
<references/>
Investigating the structural basis of purine specificity in the structures of MS2 coat protein RNA translational operator hairpins., Helgstrand C, Grahn E, Moss T, Stonehouse NJ, Tars K, Stockley PG, Liljas L, Nucleic Acids Res. 2002 Jun 15;30(12):2678-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12060685 12060685]
__TOC__
[[Category: Enterobacterio phage ms2]]
</StructureSection>
[[Category: Single protein]]
[[Category: Escherichia phage MS2]]
[[Category: Grahn, E.]]
[[Category: Large Structures]]
[[Category: Helgstrand, C.]]
[[Category: Grahn E]]
[[Category: Liljas, L.]]
[[Category: Helgstrand C]]
[[Category: Stockley, P.G.]]
[[Category: Liljas L]]
[[Category: Stonehouse, N.J.]]
[[Category: Stockley PG]]
[[Category: capsid]]
[[Category: Stonehouse NJ]]
[[Category: complex (capsid protein/rna hairpin)]]
[[Category: hairpin]]
[[Category: levivirus]]
[[Category: virus]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 12:28:17 2007''

Latest revision as of 09:41, 1 May 2024

MS2-RNA HAIRPIN (C-7) COMPLEXMS2-RNA HAIRPIN (C-7) COMPLEX

Structural highlights

2iz8 is a 5 chain structure with sequence from Escherichia phage MS2. This structure supersedes the now removed PDB entry 1gkv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.3Å
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.

See Also

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

2iz8, resolution 3.30Å

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