4yg6: Difference between revisions

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 ==Structural basis of glycan recognition in neonate-specific rotaviruses==
-<StructureSection load='4yg6' size='340' side='right' caption='[[4yg6]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
+<StructureSection load='4yg6' size='340' side='right'caption='[[4yg6]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4yg6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YG6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YG6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4yg6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rotavirus_A_RVA/Cow-tc/USA/B223/1983/G10P11 Rotavirus A RVA/Cow-tc/USA/B223/1983/G10P11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YG6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YG6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.46&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yg3|4yg3]], [[4ye2|4ye2]], [[4yfw|4yfw]], [[4yfz|4yfz]], [[4yg0|4yg0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4yg6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yg6 OCA], [http://pdbe.org/4yg6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yg6 RCSB], [http://www.ebi.ac.uk/pdbsum/4yg6 PDBsum]</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=4yg6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yg6 OCA], [https://pdbe.org/4yg6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yg6 RCSB], [https://www.ebi.ac.uk/pdbsum/4yg6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yg6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VP4_ROTBB VP4_ROTBB]] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. Rotavirus entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. According to the considered strain, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1 (By similarity).  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 (By similarity).  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 (By similarity).
+[https://www.uniprot.org/uniprot/VP4_ROTSH VP4_ROTSH] Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence (PubMed:1649333). Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors (PubMed:9144247, PubMed:15165605). It is subsequently lost, together with VP7, following virus entry into the host cell (PubMed:15165605). Following entry into the host cell, low intracellular or intravesicular Ca(2+) concentration probably causes the calcium-stabilized VP7 trimers to dissociate from the virion. This step is probably necessary for the membrane-disrupting entry step and the release of VP4, which is locked onto the virion by VP7. During the virus exit from the host cell, VP4 seems to be required to target the newly formed virions to the host cell lipid rafts (By similarity).[HAMAP-Rule:MF_04132]<ref>PMID:1649333</ref> <ref>PMID:9144247</ref> <ref>PMID:15165605</ref>   Forms the spike 'foot' and 'body' and acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. During entry, the part of VP5* that protrudes from the virus folds back on itself and reorganizes from a local dimer to a trimer. This reorganization may be linked to membrane penetration by exposing VP5* hydrophobic region. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment.[HAMAP-Rule:MF_04132]  Forms the head of the spikes and mediates the recognition of specific host cell surface glycans. 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. In some other strains, VP8* mediates the attachment to histo-blood group antigens (HBGAs) for viral entry.[HAMAP-Rule:MF_04132]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 4yg6" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hu, L]]
+[[Category: Large Structures]]
-[[Category: Prasad, B V.V]]
+[[Category: Hu L]]
-[[Category: Glycan]]
+[[Category: Prasad BVV]]
-[[Category: Rotavirus]]
-[[Category: Structural biology]]
-[[Category: Viral protein]]