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| | <StructureSection load='5kw9' size='340' side='right'caption='[[5kw9]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='5kw9' size='340' side='right'caption='[[5kw9]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5kw9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Norwalk_calicivirus Norwalk calicivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KW9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5kw9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Norwalk_virus Norwalk virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KW9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.3Å</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=5kw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kw9 OCA], [http://pdbe.org/5kw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kw9 RCSB], [http://www.ebi.ac.uk/pdbsum/5kw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kw9 ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5kw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kw9 OCA], [https://pdbe.org/5kw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kw9 RCSB], [https://www.ebi.ac.uk/pdbsum/5kw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kw9 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CAPSD_NVN68 CAPSD_NVN68]] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.<ref>PMID:16840313</ref> Soluble capsid protein may play a role in viral immunoevasion.<ref>PMID:16840313</ref> | + | [https://www.uniprot.org/uniprot/CAPSD_NVN68 CAPSD_NVN68] Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.<ref>PMID:16840313</ref> Soluble capsid protein may play a role in viral immunoevasion.<ref>PMID:16840313</ref> |
| | <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 5kw9" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5kw9" 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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| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Norwalk calicivirus]] | + | [[Category: Norwalk virus]] |
| - | [[Category: Prasad, B V.V]] | + | [[Category: Prasad BVV]] |
| - | [[Category: Shanker, S]] | + | [[Category: Shanker S]] |
| - | [[Category: Antibody]]
| + | |
| - | [[Category: Antiviral protein]]
| + | |
| - | [[Category: Fab]]
| + | |
| - | [[Category: Iga]]
| + | |
| - | [[Category: Neutralisation]]
| + | |
| - | [[Category: Norovirus]]
| + | |
| Structural highlights
Function
CAPSD_NVN68 Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. A smaller form of capsid with a diameter of 23 nm might be capsid proteins assembled as icosahedron with T=1 symmetry. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells.[1] Soluble capsid protein may play a role in viral immunoevasion.[2]
Publication Abstract from PubMed
Human noroviruses (HuNoVs) cause sporadic and epidemic gastroenteritis worldwide. They are classified into two major genogroups (GI and GII), with each genogroup further divided into multiple genotypes. Susceptibility to these viruses is influenced by genetically determined histo-blood group antigen (HBGA) expression. HBGAs function as cell attachment factors by binding to a surface-exposed region in the protruding (P) domain of the capsid protein. Sequence variations in this region that result in differential HBGA binding patterns and antigenicity are suggested to form a basis for strain diversification. Recent studies show that serum antibodies that block HBGA binding correlate with protection against illness. Although genogroup-dependent variation in HBGA binding specificity is structurally well characterized, an understanding of how antibodies block HBGA binding and how genotypic variations affect such blockade is lacking. Our crystallographic studies of the GI.1 P domain in complex with the Fab fragment of a human IgA monoclonal antibody (IgA 5I2) with HBGA blocking activity show that the antibody recognizes a conformational epitope formed by two surface-exposed loop clusters in the P domain. The antibody engulfs the HBGA binding site but does not affect its structural integrity. An unusual feature of the antigen recognition by IgA 5I2 is the predominant involvement of the CDR light chain 1 in contrast to the commonly observed CDR heavy chain 3, providing a unique perspective into antibody diversity in antigen recognition. Identification of the antigenic site in the P domain shows how genotypic variations might allow escape from antibody neutralization and exemplifies the interplay between antigenicity and HBGA specificity in HuNoV evolution.
Structural basis for norovirus neutralization by an HBGA blocking human IgA antibody.,Shanker S, Czako R, Sapparapu G, Alvarado G, Viskovska M, Sankaran B, Atmar RL, Crowe JE Jr, Estes MK, Prasad BV Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201609990. PMID:27647885[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tan M, Meller J, Jiang X. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein. J Virol. 2006 Aug;80(15):7322-31. PMID:16840313 doi:http://dx.doi.org/80/15/7322
- ↑ Tan M, Meller J, Jiang X. C-terminal arginine cluster is essential for receptor binding of norovirus capsid protein. J Virol. 2006 Aug;80(15):7322-31. PMID:16840313 doi:http://dx.doi.org/80/15/7322
- ↑ Shanker S, Czako R, Sapparapu G, Alvarado G, Viskovska M, Sankaran B, Atmar RL, Crowe JE Jr, Estes MK, Prasad BV. Structural basis for norovirus neutralization by an HBGA blocking human IgA antibody. Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201609990. PMID:27647885 doi:http://dx.doi.org/10.1073/pnas.1609990113
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