2iz9: Difference between revisions

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 ==MS2-RNA HAIRPIN (4ONE -5) COMPLEX==
-<StructureSection load='2iz9' size='340' side='right' caption='[[2iz9]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+<StructureSection load='2iz9' size='340' side='right'caption='[[2iz9]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2iz9]] is a 5 chain structure with sequence from [http://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=1dzs 1dzs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IZ9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2iz9]] 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=1dzs 1dzs]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IZ9 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ONE:1-(BETA-D-RIBOFURANOSYL)-PYRIDIN-4-ONE-5-PHOSPHATE'>ONE</scene></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]] 2.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[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]], [[2iz8|2iz8]], [[2izm|2izm]], [[2izn|2izn]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ONE:1-(BETA-D-RIBOFURANOSYL)-PYRIDIN-4-ONE-5-PHOSPHATE'>ONE</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2iz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iz9 OCA], [http://pdbe.org/2iz9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2iz9 RCSB], [http://www.ebi.ac.uk/pdbsum/2iz9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2iz9 ProSAT]</span></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=2iz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iz9 OCA], [https://pdbe.org/2iz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iz9 RCSB], [https://www.ebi.ac.uk/pdbsum/2iz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iz9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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]]
@@ Line 20: / Line 20: @@
 </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=2iz9 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The MS2 coat protein binds specifically to an RNA hairpin formed within the viral genome. By soaking different RNA fragments into crystals of MS2 coat protein capsids it is possible to determine the X-ray structure of the RNA-protein complexes formed. Here we present the structure to 2.85 A resolution of a complex between a chemically modified RNA hairpin variant and the MS2 coat protein. This RNA variant has a substitution at the -5 base position, which has been shown previously to be pyrimidine-specific and is a uracil in the wild-type RNA. The modified RNA hairpin contains a pyridin-4-one base (4one) at this position that lacks the exocyclic 2-oxygen eliminating the possibility of forming a hydrogen bond to asparagine A87 in the protein. The 4one complex structure shows an unprecedented major conformational change in the loop region of the RNA, whereas there is almost no change in the conformation of the protein.
-Deletion of a single hydrogen bonding atom from the MS2 RNA operator leads to dramatic rearrangements at the RNA-coat protein interface.,Grahn E, Stonehouse NJ, Adams CJ, Fridborg K, Beigelman L, Matulic-Adamic J, Warriner SL, Stockley PG, Liljas L Nucleic Acids Res. 2000 Dec 1;28(23):4611-6. PMID:11095669<ref>PMID:11095669</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 2iz9" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteriophage ms2]]
+[[Category: Escherichia phage MS2]]
-[[Category: Adams, C J]]
+[[Category: Large Structures]]
-[[Category: Beigelman, L]]
+[[Category: Adams CJ]]
-[[Category: Fridborg, K]]
+[[Category: Beigelman L]]
-[[Category: Grahn, E]]
+[[Category: Fridborg K]]
-[[Category: Liljas, L]]
+[[Category: Grahn E]]
-[[Category: Matulic-Adamic, J]]
+[[Category: Liljas L]]
-[[Category: Stockley, P G]]
+[[Category: Matulic-Adamic J]]
-[[Category: Stonehouse, N J]]
+[[Category: Stockley PG]]
-[[Category: Warriner, S L]]
+[[Category: Stonehouse NJ]]
-[[Category: Capsid]]
+[[Category: Warriner SL]]
-[[Category: Hairpin]]
-[[Category: Levivirus]]
-[[Category: Virus]]
-[[Category: Virus-rna complex]]
-[[Category: Virus/rna]]