2izw: Difference between revisions

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OCA

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-[[Image:2izw.jpg|left|200px]]<br /><applet load="2izw" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2izw, resolution 2.90&Aring;" />
-'''CRYSTAL STRUCTURE OF RYEGRASS MOTTLE VIRUS'''<br />
-==Overview==
+==Crystal structure of Ryegrass Mottle Virus==
-The crystal structure of the sobemovirus Ryegrass mottle virus (RGMoV) has, been determined at 2.9 A resolution. The coat protein has a canonical, jellyroll beta-sandwich fold. In comparison to other sobemoviruses the, RGMoV coat protein is missing several residues in two of the loop regions., The first loop contributes to contacts between subunits around the, quasi-threefold symmetry axis. The altered contact interface results in, tilting of the subunits towards the quasi-threefold axis. The assembly of, the T=3 capsid of sobemoviruses is controlled by the N-termini of C, subunits forming a so-called beta-annulus. The other loop that is smaller, in the RGMoV structure contains a helix that participates in stabilization, of the beta-annulus in other sobemoviruses. The loss of interaction, between the RGMoV loop and the beta-annulus has been compensated for by, additional interactions between the N-terminal arms. As a consequence of, these differences, the diameter of the RGMoV particle is 8 A smaller than, that of the other sobemoviruses. The interactions of coat proteins in, sobemovirus capsids involve calcium ions. Depletion of calcium ions, results in particle swelling, which is considered a first step in, disassembly. We could not identify any density for metal ions in the, proximity of the conserved residues normally involved in calcium binding, but the RGMoV structure does not show any signs of swelling. A likely, reason is the low pH (3.0) of the crystallization buffer in which the, groups interacting with the calcium ions are not charged.
+<StructureSection load='2izw' size='340' side='right'caption='[[2izw]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2izw]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ryegrass_mottle_virus Ryegrass mottle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IZW 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]] 2.9&#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=2izw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2izw OCA], [https://pdbe.org/2izw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2izw RCSB], [https://www.ebi.ac.uk/pdbsum/2izw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2izw ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9E962_9VIRU Q9E962_9VIRU]
+== 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/2izw_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=2izw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the sobemovirus Ryegrass mottle virus (RGMoV) has been determined at 2.9 A resolution. The coat protein has a canonical jellyroll beta-sandwich fold. In comparison to other sobemoviruses the RGMoV coat protein is missing several residues in two of the loop regions. The first loop contributes to contacts between subunits around the quasi-threefold symmetry axis. The altered contact interface results in tilting of the subunits towards the quasi-threefold axis. The assembly of the T=3 capsid of sobemoviruses is controlled by the N-termini of C subunits forming a so-called beta-annulus. The other loop that is smaller in the RGMoV structure contains a helix that participates in stabilization of the beta-annulus in other sobemoviruses. The loss of interaction between the RGMoV loop and the beta-annulus has been compensated for by additional interactions between the N-terminal arms. As a consequence of these differences, the diameter of the RGMoV particle is 8 A smaller than that of the other sobemoviruses. The interactions of coat proteins in sobemovirus capsids involve calcium ions. Depletion of calcium ions results in particle swelling, which is considered a first step in disassembly. We could not identify any density for metal ions in the proximity of the conserved residues normally involved in calcium binding, but the RGMoV structure does not show any signs of swelling. A likely reason is the low pH (3.0) of the crystallization buffer in which the groups interacting with the calcium ions are not charged.
-==About this Structure==
+The three-dimensional structure of ryegrass mottle virus at 2.9 A resolution.,Plevka P, Tars K, Zeltins A, Balke I, Truve E, Liljas L Virology. 2007 Dec 20;369(2):364-74. Epub 2007 Sep 19. PMID:17881031<ref>PMID:17881031</ref>
-IZW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ryegrass_mottle_virus Ryegrass mottle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IZW OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The three-dimensional structure of ryegrass mottle virus at 2.9 A resolution., Plevka P, Tars K, Zeltins A, Balke I, Truve E, Liljas L, Virology. 2007 Sep 17;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17881031 17881031]
+</div>
+<div class="pdbe-citations 2izw" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Ryegrass mottle virus]]
-[[Category: Single protein]]
+[[Category: Balke I]]
-[[Category: Balke, I.]]
+[[Category: Liljas L]]
-[[Category: Liljas, L.]]
+[[Category: Plevka P]]
-[[Category: Plevka, P.]]
+[[Category: Tars K]]
-[[Category: Tars, K.]]
+[[Category: Truve E]]
-[[Category: Truve, E.]]
+[[Category: Zeltins A]]
-[[Category: Zeltins, A.]]
-[[Category: assembly]]
-[[Category: capsid protein]]
-[[Category: rna]]
-[[Category: virus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:56:51 2008''