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| | ==Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactosamine== | | ==Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactosamine== |
| - | <StructureSection load='4mbz' size='340' side='right' caption='[[4mbz]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='4mbz' size='340' side='right'caption='[[4mbz]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mbz]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/B-lymphotropic_polyomavirus B-lymphotropic polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MBZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mbz]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/B-lymphotropic_polyomavirus B-lymphotropic polyomavirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MBZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900067:3-sialyl-N-acetyllactosamine'>PRD_900067</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></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=4mbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbz OCA], [https://pdbe.org/4mbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mbz RCSB], [https://www.ebi.ac.uk/pdbsum/4mbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbz ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mbx|4mbx]], [[4mby|4mby]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=332091 B-lymphotropic polyomavirus])</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=4mbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mbz OCA], [http://pdbe.org/4mbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mbz RCSB], [http://www.ebi.ac.uk/pdbsum/4mbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mbz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/VP1_POVLY VP1_POVLY] 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 a N-linked glycoprotein containing sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by 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.[UniProtKB:P03087] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4mbz" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4mbz" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: B-lymphotropic polyomavirus]] | | [[Category: B-lymphotropic polyomavirus]] |
| - | [[Category: Khan, Z M]] | + | [[Category: Large Structures]] |
| - | [[Category: Neu, U]] | + | [[Category: Khan ZM]] |
| - | [[Category: Stehle, T]] | + | [[Category: Neu U]] |
| - | [[Category: Dna encapsidation]] | + | [[Category: Stehle T]] |
| - | [[Category: Jelly roll]]
| + | |
| - | [[Category: Polyomavirus]]
| + | |
| - | [[Category: Receptor binding]]
| + | |
| - | [[Category: Sialylated oligosaccharide]]
| + | |
| - | [[Category: Viral protein]]
| + | |
| Structural highlights
4mbz is a 10 chain structure with sequence from B-lymphotropic polyomavirus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
VP1_POVLY 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 a N-linked glycoprotein containing sialic acids on the cell surface to provide virion attachment to target cell. Once attached, the virion is internalized by 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.[UniProtKB:P03087]
Publication Abstract from PubMed
B-Lymphotropic Polyomavirus (LPyV) serves as a paradigm of virus receptor binding and tropism, and is the closest relative of the recently discovered Human Polyomavirus 9 (HPyV9). LPyV infection depends on sialic acid on host cells, but the molecular interactions underlying LPyV-receptor binding were unknown. We find by glycan array screening that LPyV specifically recognizes a linear carbohydrate motif that contains alpha2,3-linked sialic acid. High-resolution crystal structures of the LPyV capsid protein VP1 alone and in complex with the trisaccharide ligands 3'-sialyllactose and 3'-sialyl-N-acetyl-lactosamine (3SL and 3SLN, respectively) show essentially identical interactions. Most contacts are contributed by the sialic acid moiety, which is almost entirely buried in a narrow, preformed cleft at the outer surface of the capsid. The recessed nature of the binding site on VP1 and the nature of the observed glycan interactions differ from those of related polyomaviruses and most other sialic acid-binding viruses, which bind sialic acid in shallow, more exposed grooves. Despite their different modes for recognition, the sialic acid binding sites of LPyV and SV40 are half-conserved, hinting at an evolutionary strategy for diversification of binding sites. Our analysis provides a structural basis for the observed specificity of LPyV for linear glycan motifs terminating in alpha2,3-linked sialic acid, and links the different tropisms of known LPyV strains to the receptor binding site. It also serves as a useful template for understanding the ligand-binding properties and serological crossreactivity of HPyV9.
Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands.,Neu U, Khan ZM, Schuch B, Palma AS, Liu Y, Pawlita M, Feizi T, Stehle T PLoS Pathog. 2013 Oct;9(10):e1003714. doi: 10.1371/journal.ppat.1003714. Epub, 2013 Oct 31. PMID:24204265[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Neu U, Khan ZM, Schuch B, Palma AS, Liu Y, Pawlita M, Feizi T, Stehle T. Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. PLoS Pathog. 2013 Oct;9(10):e1003714. doi: 10.1371/journal.ppat.1003714. Epub, 2013 Oct 31. PMID:24204265 doi:http://dx.doi.org/10.1371/journal.ppat.1003714
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