3ast: Difference between revisions
New page: '''Unreleased structure''' The entry 3ast is ON HOLD Authors: Kubota, T., Kumagai, A., Itoh, H., Furukawa, S., Narimatsu, H., Wakita, T., Ishii, K., Takeda, N., Someya, Y., Shirato, H. ... |
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==Crystal structure of P domain Q389N mutant from Norovirus Funabashi258 stain in the complex with Lewis-b== | |||
<StructureSection load='3ast' size='340' side='right'caption='[[3ast]], [[Resolution|resolution]] 1.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ast]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norwalk-like_virus Norwalk-like virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AST OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AST FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene>, <scene name='pdbligand=PRD_900123:Lewis+B+antigen,+beta+anomer'>PRD_900123</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=3ast FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ast OCA], [https://pdbe.org/3ast PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ast RCSB], [https://www.ebi.ac.uk/pdbsum/3ast PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ast ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8JW44_9CALI Q8JW44_9CALI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Noroviruses (NoVs) bind to histo-blood group antigens, namely, ABH antigens and Lewis antigens. We previously showed the NoVs GI/2, GI/3, GI/4, and GI/8 were able to strongly bind to Lewis a (Le(a)) antigen, which is expressed by individuals who are nonsecretors. In this study, to investigate how Lewis antigens interact with GI NoV virion protein 1 (VP1), we determined the crystal structures of the P domain of the VP1 protein from the Funabashi 258 (FUV258) strain (GI/2) in complexes with Le(a), Le(b), H type 1, or A type 1 antigens. The structures were compared with those of the NV/68 strain (GI/1), which does not bind to the Le(a) antigen. The four loop structures, loop P, loop S, loop A, and loop B, continuously deviated by more than 2 A in length between the Calpha atoms of the corresponding residues of the FUV258 and NV/68 P domains. The most pronounced differences between the two VP1 proteins were observed in the structures of loop P. In the FUV258 P domain, loop P protruded toward the next protomer, forming a Le(a) antigen-binding site. The Gln389 residue make a significant contribution to the binding of the Le(a) antigen through the stabilization of loop P as well as through direct interactions with the alpha4-fucosyl residue (alpha4Fuc) of the Le(a) antigen. Mutation of the Gln389 residue dramatically affected the degree of binding of the Lewis antigens. Collectively, these results suggest that loop P and the amino acid residue at position 389 affect Lewis antigen binding. | |||
Structural basis for the recognition of Lewis antigens by genogroup I norovirus.,Kubota T, Kumagai A, Ito H, Furukawa S, Someya Y, Takeda N, Ishii K, Wakita T, Narimatsu H, Shirato H J Virol. 2012 Oct;86(20):11138-50. Epub 2012 Aug 1. PMID:22855491<ref>PMID:22855491</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ast" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Norwalk-like virus]] | |||
[[Category: Furukawa S]] | |||
[[Category: Ishii K]] | |||
[[Category: Itoh H]] | |||
[[Category: Kubota T]] | |||
[[Category: Kumagai A]] | |||
[[Category: Narimatsu H]] | |||
[[Category: Shirato H]] | |||
[[Category: Someya Y]] | |||
[[Category: Takeda N]] | |||
[[Category: Wakita T]] | |||
Latest revision as of 18:54, 4 October 2023
Crystal structure of P domain Q389N mutant from Norovirus Funabashi258 stain in the complex with Lewis-bCrystal structure of P domain Q389N mutant from Norovirus Funabashi258 stain in the complex with Lewis-b
Structural highlights
FunctionPublication Abstract from PubMedNoroviruses (NoVs) bind to histo-blood group antigens, namely, ABH antigens and Lewis antigens. We previously showed the NoVs GI/2, GI/3, GI/4, and GI/8 were able to strongly bind to Lewis a (Le(a)) antigen, which is expressed by individuals who are nonsecretors. In this study, to investigate how Lewis antigens interact with GI NoV virion protein 1 (VP1), we determined the crystal structures of the P domain of the VP1 protein from the Funabashi 258 (FUV258) strain (GI/2) in complexes with Le(a), Le(b), H type 1, or A type 1 antigens. The structures were compared with those of the NV/68 strain (GI/1), which does not bind to the Le(a) antigen. The four loop structures, loop P, loop S, loop A, and loop B, continuously deviated by more than 2 A in length between the Calpha atoms of the corresponding residues of the FUV258 and NV/68 P domains. The most pronounced differences between the two VP1 proteins were observed in the structures of loop P. In the FUV258 P domain, loop P protruded toward the next protomer, forming a Le(a) antigen-binding site. The Gln389 residue make a significant contribution to the binding of the Le(a) antigen through the stabilization of loop P as well as through direct interactions with the alpha4-fucosyl residue (alpha4Fuc) of the Le(a) antigen. Mutation of the Gln389 residue dramatically affected the degree of binding of the Lewis antigens. Collectively, these results suggest that loop P and the amino acid residue at position 389 affect Lewis antigen binding. Structural basis for the recognition of Lewis antigens by genogroup I norovirus.,Kubota T, Kumagai A, Ito H, Furukawa S, Someya Y, Takeda N, Ishii K, Wakita T, Narimatsu H, Shirato H J Virol. 2012 Oct;86(20):11138-50. Epub 2012 Aug 1. PMID:22855491[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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