This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.


Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5vki

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:50, 4 October 2023) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2==
==Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2==
-
<StructureSection load='5vki' size='340' side='right' caption='[[5vki]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+
<StructureSection load='5vki' size='340' side='right'caption='[[5vki]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5vki]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VKI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VKI FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5vki]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rotavirus_A Human rotavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VKI FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THR:THREONINE'>THR</scene></td></tr>
+
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vks|5vks]]</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THR:THREONINE'>THR</scene></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vki OCA], [http://pdbe.org/5vki PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vki RCSB], [http://www.ebi.ac.uk/pdbsum/5vki PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vki ProSAT]</span></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=5vki FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vki OCA], [https://pdbe.org/5vki PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vki RCSB], [https://www.ebi.ac.uk/pdbsum/5vki PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vki ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/A7YCM0_9REOV A7YCM0_9REOV]] Outer capsid protein VP5*: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.[SAAS:SAAS00846030] VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact.[SAAS:SAAS00846016]
+
[https://www.uniprot.org/uniprot/A7YCM0_9VIRU A7YCM0_9VIRU]
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Recognition of specific cell surface glycans, mediated by the VP8* domain of the spike protein VP4, is the essential first step in rotavirus (RV) infection. Due to lack of direct structural information of virus-ligand interactions, the molecular basis of ligand-controlled host ranges of the major human RVs (P[8] and P[4]) in P[II] genogroup remains unknown. Here, through characterization of a minor P[II] RV (P[19]) that can infect both animals (pigs) and humans, we made an important advance to fill this knowledge gap by solving the crystal structures of the P[19] VP8* in complex with its ligands. Our data showed that P[19] RVs use a novel binding site that differs from the known ones of other genotypes/genogroups. This binding site is capable of interacting with two types of glycans, the mucin core and type 1 histo-blood group antigens (HBGAs) with a common GlcNAc as the central binding saccharide. The binding site is apparently shared by other P[II] RVs and possibly two genotypes (P[10] and P[12]) in P[I] as shown by their highly conserved GlcNAc-interacting residues. These data provide strong evidence of evolutionary connections among these human and animal RVs, pointing to a common ancestor in P[I] with a possible animal host origin. While the binding properties to GlcNAc-containing saccharides are maintained, changes in binding to additional residues, such as those in the polymorphic type 1 HBGAs may occur in the course of RV evolution, explaining the complex P[II] genogroup that mainly causes diseases in humans but also in some animals.
 +
 
 +
Structural basis of glycan specificity of P[19] VP8*: Implications for rotavirus zoonosis and evolution.,Liu Y, Xu S, Woodruff AL, Xia M, Tan M, Kennedy MA, Jiang X PLoS Pathog. 2017 Nov 14;13(11):e1006707. doi: 10.1371/journal.ppat.1006707., eCollection 2017 Nov. PMID:29136651<ref>PMID:29136651</ref>
 +
 
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 5vki" style="background-color:#fffaf0;"></div>
 +
 
 +
==See Also==
 +
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 +
== References ==
 +
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Jiang, X]]
+
[[Category: Human rotavirus A]]
-
[[Category: Kennedy, M A]]
+
[[Category: Large Structures]]
-
[[Category: Liu, Y]]
+
[[Category: Jiang X]]
-
[[Category: Woodruff, A]]
+
[[Category: Kennedy MA]]
-
[[Category: Xu, S]]
+
[[Category: Liu Y]]
-
[[Category: Zhong, W]]
+
[[Category: Woodruff A]]
-
[[Category: Complex]]
+
[[Category: Xu S]]
-
[[Category: Mucin core 2]]
+
[[Category: Zhong W]]
-
[[Category: Viral protein]]
+

Current revision

Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2

PDB ID 5vki

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools