3q39

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<StructureSection load='3q39' size='340' side='right'caption='[[3q39]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
<StructureSection load='3q39' size='340' side='right'caption='[[3q39]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q39]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norwalk_calicivirus Norwalk calicivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q39 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q39]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norwalk_virus Norwalk virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q39 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r6j|3r6j]], [[3r6k|3r6k]], [[3pa1|3pa1]], [[3pa2|3pa2]], [[3q38|3q38]], [[3q3a|3q3a]], [[3q6q|3q6q]], [[3q6r|3q6r]], [[3ony|3ony]], [[3onu|3onu]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Capsid protein ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11983 Norwalk calicivirus])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q39 OCA], [https://pdbe.org/3q39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q39 RCSB], [https://www.ebi.ac.uk/pdbsum/3q39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q39 ProSAT]</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=3q39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q39 OCA], [https://pdbe.org/3q39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q39 RCSB], [https://www.ebi.ac.uk/pdbsum/3q39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q39 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q5F4T5_9CALI Q5F4T5_9CALI]
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Noroviruses are the dominant cause of outbreaks of gastroenteritis worldwide, and interactions with human histo-blood group antigens (HBGAs) are thought to play a critical role in their entry mechanism. Structures of noroviruses from genogroups GI and GII in complex with HBGAs, however, reveal different modes of interaction. To gain insight into norovirus recognition of HBGAs, we determined crystal structures of norovirus protruding domains from two rarely detected GII genotypes, GII.10 and GII.12, alone and in complex with a panel of HBGAs, and analyzed structure-function implications related to conservation of the HBGA-binding pocket. The GII.10- and GII.12-apo structures as well as the previously solved GII.4-apo structure resembled each other more closely than the GI.1-derived one, and all three GII structures showed similar modes of HBGA recognition. The primary GII norovirus-HBGA interaction involved six hydrogen bonds between a terminal alphafucose1-2 of the HBGAs and a dimeric capsid interface, which was composed of elements from two protruding subdomains. Norovirus interactions with other saccharide units of the HBGAs were variable and involved fewer hydrogen bonds, some of which were water-mediated. Sequence analysis revealed a site of GII norovirus-sequence conservation to reside under the critical alphafucose1-2 and to be one of the few patches of conserved residues on the outer virion-capsid surface. The site was smaller than involved in full HBGA recognition, a consequence of variable recognition of peripheral saccharides. Despite this evasion tactic, the HBGA site of viral vulnerability may provide a viable target for small molecule- and antibody-mediated neutralization of GII norovirus.
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Crystal Structures of GII.10 and GII.12 Norovirus Protruding Domains in Complex with Histo-Blood Group Antigens Reveal Details for a Potential Site of Vulnerability.,Hansman GS, Biertumpfel C, Georgiev I, McLellan JS, Chen L, Zhou T, Katayama K, Kwong PD J Virol. 2011 Apr 27. PMID:21525337<ref>PMID:21525337</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3q39" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Norwalk calicivirus]]
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[[Category: Norwalk virus]]
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[[Category: Biertumpfel, C]]
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[[Category: Biertumpfel C]]
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[[Category: Chen, L]]
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[[Category: Chen L]]
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[[Category: Georgiev, I]]
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[[Category: Georgiev I]]
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[[Category: Hansman, G S]]
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[[Category: Hansman GS]]
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[[Category: Katayama, K]]
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[[Category: Katayama K]]
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[[Category: Kwong, P D]]
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[[Category: Kwong PD]]
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[[Category: McLellan, J S]]
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[[Category: McLellan JS]]
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[[Category: Capsid]]
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[[Category: Norovirus]]
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[[Category: P-domain]]
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[[Category: Receptor]]
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[[Category: Viral protein]]
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Current revision

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type H2 (diglycan)

PDB ID 3q39

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