1sva: Difference between revisions

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-[[Image:1sva.gif|left|200px]]<br /><applet load="1sva" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1sva, resolution 3.1&Aring;" />
-'''SIMIAN VIRUS 40'''<br />
-==Overview==
+==SIMIAN VIRUS 40==
-BACKGROUND: The structure of simian virus 40 (SV40), previously determined at 3.8 degree resolution, shows how its pentameric VP1 assembly units are tied together by extended C-terminal arms. In order to define more precisely the possible assembly mechanisms, we have refined the structure at 3.1 degree resolution. RESULTS: New data from a high-intensity synchrotron source have been used for phase extension by electron-density averaging and refinement, exploiting only the strict 5-fold non-crystallographic symmetry for the real-space averaging steps. The accurate model enables us to study important structural features of the virus particle in detail. The remarkably invariant core of the VP1 pentamer bears the docking sites for the C-terminal arms from other pentamers. These contacts are the principal way in which pentameric assembly units are linked together in the capsid. Only at the interface between five-coordinated and six-coordinated pentamers do the pentamer cores appear to interact strongly. There are two cation-binding sites per VP1 monomer, seen in a soaking experiment with gadolinium nitrate. These sites are quite close to each other at the interfaces between pentamers. CONCLUSION: We propose that the contact between five-coordinated and six-coordinated pentamers may help to generate a six-pentamer nucleus, with which further pentamers can assemble to generate the complete particle. Calcium ions probably stabilize the structure of the assembled particle, rather than direct its assembly.
+<SX load='1sva' size='340' side='right' viewer='molstar' caption='[[1sva]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1sva]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Macaca_mulatta_polyomavirus_1 Macaca mulatta polyomavirus 1]. The November 2003 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Simian Virus 40''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2003_11 10.2210/rcsb_pdb/mom_2003_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SVA 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]] 3.1&#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=1sva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sva OCA], [https://pdbe.org/1sva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sva RCSB], [https://www.ebi.ac.uk/pdbsum/1sva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sva ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VP1_SV40 VP1_SV40] Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Binds to N-glycolylneuraminic analog of the ganglioside GM1 on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. The assembly takes place in the cell nucleus. Encapsulates the genomic DNA and participates in rearranging nucleosomes around the viral DNA. The viral progenies exit the cells by lytic release.
+== 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/sv/1sva_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=1sva ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-SVA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Simian_virus_40 Simian virus 40]. The following page contains interesting information on the relation of 1SVA with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb47_1.html Simian Virus 40]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SVA OCA].
+*[[Art:Pentagonal Garden|Art:Pentagonal Garden]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-==Reference==
+__TOC__
-The structure of simian virus 40 refined at 3.1 A resolution., Stehle T, Gamblin SJ, Yan Y, Harrison SC, Structure. 1996 Feb 15;4(2):165-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8805523 8805523]
+</SX>
+[[Category: Large Structures]]
+[[Category: Macaca mulatta polyomavirus 1]]
+[[Category: RCSB PDB Molecule of the Month]]
 [[Category: Simian Virus 40]]
-[[Category: Simian virus 40]]
+[[Category: Gamblin SJ]]
-[[Category: Single protein]]
+[[Category: Harrison SC]]
-[[Category: Gamblin, S J.]]
+[[Category: Stehle T]]
-[[Category: Harrison, S C.]]
-[[Category: Stehle, T.]]
-[[Category: icosahedral virus]]
-[[Category: virus coat protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:05:35 2008''