2vf9: Difference between revisions

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-{{Seed}}
-[[Image:2vf9.jpg|left|200px]]
-<!--
+==Crystal structure of bacteriophage PRR1==
-The line below this paragraph, containing "STRUCTURE_2vf9", creates the "Structure Box" on the page.
+<StructureSection load='2vf9' size='340' side='right'caption='[[2vf9]], [[Resolution|resolution]] 3.50&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'>[[2vf9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_phage_PRR1 Pseudomonas phage PRR1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VF9 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]] 3.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-{{STRUCTURE_2vf9|  PDB=2vf9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vf9 OCA], [https://pdbe.org/2vf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vf9 RCSB], [https://www.ebi.ac.uk/pdbsum/2vf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vf9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COAT_BPPRR COAT_BPPRR] Forms the phage shell; binds to the phage RNA.
+== 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/vf/2vf9_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=2vf9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Many nonenveloped virus particles are stabilized by calcium ions bound in the interfaces between the protein subunits. These ions may have a role in the disassembly process. The small RNA phages of the Leviviridae family have T=3 quasi-symmetry and are unique among simple viruses in that they have a coat protein with a translational repressor activity and a fold that has not been observed in other viruses. The crystal structure of phage PRR1 has been determined to 3.5 A resolution. The structure shows a tentative binding site for a calcium ion close to the quasi-3-fold axis. The RNA-binding surface used for repressor activity is mostly conserved. The structure does not show any significant differences between quasi-equivalent subunits, which suggests that the assembly is not controlled by conformational switches as in many other simple viruses.
-===CRYSTAL STRUCTURE OF BACTERIOPHAGE PRR1===
+The capsid of the small RNA phage PRR1 is stabilized by metal ions.,Persson M, Tars K, Liljas L J Mol Biol. 2008 Nov 21;383(4):914-22. Epub 2008 Aug 29. PMID:18786545<ref>PMID:18786545</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-VF9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_prr1 Pseudomonas phage prr1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VF9 OCA].
+<div class="pdbe-citations 2vf9" style="background-color:#fffaf0;"></div>
-[[Category: Pseudomonas phage prr1]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Liljas, L.]]
+__TOC__
-[[Category: Persson, M.]]
+</StructureSection>
-[[Category: Tars, K.]]
+[[Category: Large Structures]]
-[[Category: Capsid protein]]
+[[Category: Pseudomonas phage PRR1]]
-[[Category: Rna-binding]]
+[[Category: Liljas L]]
-[[Category: Structural protein]]
+[[Category: Persson M]]
-[[Category: Virion]]
+[[Category: Tars K]]
-[[Category: Virus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 24 10:34:11 2008''