1vps

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:38, 9 August 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1vps.jpg|left|200px]]
 
-
<!--
+
==POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE==
-
The line below this paragraph, containing "STRUCTURE_1vps", creates the "Structure Box" on the page.
+
<StructureSection load='1vps' size='340' side='right'caption='[[1vps]], [[Resolution|resolution]] 1.90&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'>[[1vps]] 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=1VPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VPS 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]] 1.9&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
-
{{STRUCTURE_1vps| PDB=1vps | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vps OCA], [https://pdbe.org/1vps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vps RCSB], [https://www.ebi.ac.uk/pdbsum/1vps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vps ProSAT]</span></td></tr>
 +
</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/1vps_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=1vps 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.
-
'''POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE'''
+
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>
-
 
+
-
 
+
-
==Overview==
+
-
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.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
1VPS 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=1VPS OCA].
+
</div>
 +
<div class="pdbe-citations 1vps" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
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]
+
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-
[[Category: Murine polyomavirus]]
+
== References ==
-
[[Category: Single protein]]
+
<references/>
-
[[Category: Harrison, S C.]]
+
__TOC__
-
[[Category: Stehle, T.]]
+
</StructureSection>
-
[[Category: Oligosaccharide binding]]
+
[[Category: Large Structures]]
-
[[Category: Sialic acid]]
+
[[Category: Mus musculus polyomavirus 1]]
-
[[Category: Virus assembly]]
+
[[Category: Harrison SC]]
-
[[Category: Virus coat protein]]
+
[[Category: Stehle T]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:46:24 2008''
+

Current revision

POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE

PDB ID 1vps

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vps"
Personal tools