3by2: Difference between revisions

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{{Seed}}
[[Image:3by2.png|left|200px]]


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==Norwalk P polypeptide (228-523)==
The line below this paragraph, containing "STRUCTURE_3by2", creates the "Structure Box" on the page.
<StructureSection load='3by2' size='340' side='right'caption='[[3by2]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3by2]] is a 1 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=3BY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BY2 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=3by2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3by2 OCA], [https://pdbe.org/3by2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3by2 RCSB], [https://www.ebi.ac.uk/pdbsum/3by2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3by2 ProSAT]</span></td></tr>
{{STRUCTURE_3by2|  PDB=3by2  |  SCENE=  }}
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/3by2_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3by2 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Noroviruses are positive-sense, single-stranded RNA viruses that cause acute gastroenteritis. They recognize human histo-blood group antigens as receptors in a strain-specific manner. The structures presented here were analyzed in order to elucidate the structural basis for differences in ligand recognition of noroviruses from different genogroups, the prototypic Norwalk virus (NV; GI-1) and VA387 (GII-4), which recognize the same A antigen but differ in that NV is unable to bind to the B antigen. Two forms of the receptor-binding domain of the norovirus coat protein, the P domain and the P polypeptide, that were previously shown to differ in receptor binding and P-particle formation properties were studied. Comparison of the structures of the NV P domain with and without A trisaccharide and the NV P polypeptide revealed no major ligand-induced changes. The 2.3-A cocrystal structure reveals that the A trisaccharide binds to the NV P domain through interactions with the residues Ser377, Asp327, His329, and Ser380 in a mode distinct from that previously reported for the VA387 P-domain-A-trisaccharide complex. Mutational analyses confirm the importance of these residues in NV P-particle binding to native A antigen. The alpha-GalNAc residue unique to the A trisaccharide is buried deeply in the NV binding pocket, unlike in the structures of A and B trisaccharides bound to VA387 P domain, where the alpha-fucose residue forms the most protein contacts. The A-trisaccharide binding mode seen in the NV P domain complex cannot be sterically accommodated in the VA387 P domain.


===Norwalk P polypeptide (228-523)===
Structural basis for the receptor binding specificity of Norwalk virus.,Bu W, Mamedova A, Tan M, Xia M, Jiang X, Hegde RS J Virol. 2008 Jun;82(11):5340-7. Epub 2008 Apr 2. PMID:18385236<ref>PMID:18385236</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3by2" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18385236}}, adds the Publication Abstract to the page
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18385236 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_18385236}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3BY2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Norwalk_virus Norwalk virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BY2 OCA].
 
==Reference==
<ref group="xtra">PMID:18385236</ref><references group="xtra"/>
[[Category: Norwalk virus]]
[[Category: Norwalk virus]]
[[Category: Bu, W.]]
[[Category: Bu W]]
[[Category: Hegde, R.]]
[[Category: Hegde R]]
[[Category: Norwalk virus p polypeptide]]
[[Category: Viral protein]]
 
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Retrieved from "https://proteopedia.org/3by2"