1vpn: Difference between revisions

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-{{Seed}}
-[[Image:1vpn.png|left|200px]]
-<!--
+==UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER==
-The line below this paragraph, containing "STRUCTURE_1vpn", creates the "Structure Box" on the page.
+<StructureSection load='1vpn' size='340' side='right'caption='[[1vpn]], [[Resolution|resolution]] 2.00&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'>[[1vpn]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus_polyomavirus_1 Mus musculus polyomavirus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VPN 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&#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=1vpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vpn OCA], [https://pdbe.org/1vpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vpn RCSB], [https://www.ebi.ac.uk/pdbsum/1vpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vpn ProSAT]</span></td></tr>
-{{STRUCTURE_1vpn|  PDB=1vpn  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VP1_POVMP VP1_POVMP] 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. Interacts with terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. 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. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).
+== 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/vp/1vpn_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=1vpn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of a recombinant polyomavirus VP1 pentamer (residues 32-320) in complex with a branched disialylated hexasaccharide receptor fragment has been determined at 1.9 A resolution. The result extends our understanding of oligosaccharide receptor recognition. It also suggests a mechanism for enhancing the fidelity of virus assembly. We have previously described the structure of the complete polyomavirus particle complexed with this receptor fragment at 3.65 A. The model presented here offers a much more refined view of the interactions that determine carbohydrate recognition and allows us to assign additional specific contacts, in particular those involving the (alpha2,6)-linked, branching sialic acid. The structure of the unliganded VP1 pentamer, determined independently, shows that the oligosaccharide fits into a preformed groove and induces no measurable structural rearrangements. A comparison with assembled VP1 in the virus capsid reveals a rearrangement of residues 32-45 at the base of the pentamer. This segment may help prevent the formation of incorrectly assembled particles by reducing the likelihood that the C-terminal arm will fold back into its pentamer of origin.
-===UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER===
+High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.,Stehle T, Harrison SC EMBO J. 1997 Aug 15;16(16):5139-48. PMID:9305654<ref>PMID:9305654</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1vpn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9305654}}, 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 9305654 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9305654}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-VPN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Murine_polyomavirus Murine polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VPN OCA].
+[[Category: Mus musculus polyomavirus 1]]
+[[Category: Harrison SC]]
-==Reference==
+[[Category: Stehle T]]
-High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding., Stehle T, Harrison SC, EMBO J. 1997 Aug 15;16(16):5139-48. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9305654 9305654]
-[[Category: Murine polyomavirus]]
-[[Category: Single protein]]
-[[Category: Harrison, S C.]]
-[[Category: Stehle, T.]]
-[[Category: Virus assembly]]
-[[Category: Virus coat protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 01:10:47 2008''