This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3r6k

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:12, 14 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 in complex with HBGA type B (triglycan)==
==Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 in complex with HBGA type B (triglycan)==
-
<StructureSection load='3r6k' size='340' side='right' caption='[[3r6k]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+
<StructureSection load='3r6k' size='340' side='right'caption='[[3r6k]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3r6k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R6K FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3r6k]] is a 1 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=3R6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6K FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=GLA:ALPHA+D-GALACTOSE'>GLA</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">[[3r6j|3r6j]], [[3pa1|3pa1]], [[3pa2|3pa2]], [[3q38|3q38]], [[3q39|3q39]], [[3q3a|3q3a]], [[3q6q|3q6q]], [[3q6r|3q6r]], [[3ony|3ony]], [[3onu|3onu]]</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=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Capsid protein ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10239 Viruses])</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=3r6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6k OCA], [https://pdbe.org/3r6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6k RCSB], [https://www.ebi.ac.uk/pdbsum/3r6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6k ProSAT]</span></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=3r6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r6k RCSB], [http://www.ebi.ac.uk/pdbsum/3r6k PDBsum]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q54AD6_9CALI Q54AD6_9CALI]
-
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.
+
-
 
+
-
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>
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
==See Also==
-
</div>
+
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Viruses]]
+
[[Category: Large Structures]]
-
[[Category: Biertumpfel, C]]
+
[[Category: Norwalk-like virus]]
-
[[Category: Chen, L]]
+
[[Category: Biertumpfel C]]
-
[[Category: Georgiev, I]]
+
[[Category: Chen L]]
-
[[Category: Hansman, G S]]
+
[[Category: Georgiev I]]
-
[[Category: Katayama, K]]
+
[[Category: Hansman GS]]
-
[[Category: Kwong, P D]]
+
[[Category: Katayama K]]
-
[[Category: McLellan, J S]]
+
[[Category: Kwong PD]]
-
[[Category: Zhou, T]]
+
[[Category: McLellan JS]]
-
[[Category: Capsid]]
+
[[Category: Zhou T]]
-
[[Category: Norovirus]]
+
-
[[Category: P-domain]]
+
-
[[Category: Receptor]]
+
-
[[Category: Viral protein]]
+

Current revision

Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 in complex with HBGA type B (triglycan)

PDB ID 3r6k

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3r6k"
Personal tools