3asp: Difference between revisions

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 <StructureSection load='3asp' size='340' side='right'caption='[[3asp]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3asp]] is a 2 chain structure with sequence from [http://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=3ASP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3ASP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3asp]] 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=3ASP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ASP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3asq|3asq]], [[3asr|3asr]], [[3ass|3ass]], [[3ast|3ast]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <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=PRD_900131:Blood+group+A+H+type+1+antigen,+beta+anomer'>PRD_900131</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">capsid, ORF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=95340 Norwalk like virus])</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=3asp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3asp OCA], [https://pdbe.org/3asp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3asp RCSB], [https://www.ebi.ac.uk/pdbsum/3asp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3asp ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3asp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3asp OCA], [http://pdbe.org/3asp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3asp RCSB], [http://www.ebi.ac.uk/pdbsum/3asp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3asp ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/Q8JW44_9CALI Q8JW44_9CALI]
-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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3asp" 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: Norwalk-like virus]]
-[[Category: Furukawa, S]]
+[[Category: Furukawa S]]
-[[Category: Ishii, K]]
+[[Category: Ishii K]]
-[[Category: Itoh, H]]
+[[Category: Itoh H]]
-[[Category: Kubota, T]]
+[[Category: Kubota T]]
-[[Category: Kumagai, A]]
+[[Category: Kumagai A]]
-[[Category: Narimatsu, H]]
+[[Category: Narimatsu H]]
-[[Category: Shirato, H]]
+[[Category: Shirato H]]
-[[Category: Someya, Y]]
+[[Category: Someya Y]]
-[[Category: Takeda, N]]
+[[Category: Takeda N]]
-[[Category: Wakita, T]]
+[[Category: Wakita T]]
-[[Category: Capsid protein]]
-[[Category: Histo-blood group antigen]]
-[[Category: Lectin-like protein]]
-[[Category: Protein-sugar complex]]
-[[Category: Viral protein]]