2izw: Difference between revisions

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-[[Image:2izw.png|left|200px]]
-<!--
+==Crystal structure of Ryegrass Mottle Virus==
-The line below this paragraph, containing "STRUCTURE_2izw", creates the "Structure Box" on the page.
+<StructureSection load='2izw' size='340' side='right'caption='[[2izw]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_2izw|  PDB=2izw  |  SCENE=  }}
+</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.
-===CRYSTAL STRUCTURE OF RYEGRASS MOTTLE VIRUS===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2izw" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17881031}}, adds the Publication Abstract to the page
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17881031 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17881031}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2izw]] is a 3 chain structure with 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==
-<ref group="xtra">PMID:017881031</ref><references group="xtra"/>
 [[Category: Ryegrass mottle virus]]
-[[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]]