2iz8: Difference between revisions

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 <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/Bacteriophage_ms2 Bacteriophage 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>
+<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aq3|1aq3]], [[1aq4|1aq4]], [[1bms|1bms]], [[1msc|1msc]], [[1mst|1mst]], [[1mva|1mva]], [[1mvb|1mvb]], [[1u1y|1u1y]], [[1zdh|1zdh]], [[1zdi|1zdi]], [[1zdj|1zdj]], [[1zdk|1zdk]], [[1zse|1zse]], [[2b2d|2b2d]], [[2b2e|2b2e]], [[2b2g|2b2g]], [[2bny|2bny]], [[2bq5|2bq5]], [[2bs0|2bs0]], [[2bs1|2bs1]], [[2bu1|2bu1]], [[2c4q|2c4q]], [[2c4y|2c4y]], [[2c4z|2c4z]], [[2c50|2c50]], [[2c51|2c51]], [[2ms2|2ms2]], [[5msf|5msf]], [[6msf|6msf]], [[7msf|7msf]], [[2iz9|2iz9]], [[2izm|2izm]], [[2izn|2izn]]</div></td></tr>
+</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/COAT_BPMS2 COAT_BPMS2]] Forms the phage shell; binds to the phage RNA.
+[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]]
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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=2iz8 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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:12060685<ref>PMID:12060685</ref>
+==See Also==
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2iz8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage ms2]]
+[[Category: Escherichia phage MS2]]
 [[Category: Large Structures]]
-[[Category: Grahn, E]]
+[[Category: Grahn E]]
-[[Category: Helgstrand, C]]
+[[Category: Helgstrand C]]
-[[Category: Liljas, L]]
+[[Category: Liljas L]]
-[[Category: Stockley, P G]]
+[[Category: Stockley PG]]
-[[Category: Stonehouse, N J]]
+[[Category: Stonehouse NJ]]
-[[Category: Capsid]]
-[[Category: Hairpin]]
-[[Category: Levivirus]]
-[[Category: Virus]]
-[[Category: Virus-rna complex]]
-[[Category: Virus/rna]]