2ypg: Difference between revisions

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 <StructureSection load='2ypg' size='340' side='right'caption='[[2ypg]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ypg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_a_virus_(a/x-31(h3n2)) Influenza a virus (a/x-31(h3n2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YPG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ypg]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/X-31(H3N2)) Influenza A virus (A/X-31(H3N2))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YPG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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]] 2.85&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</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=2ypg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ypg OCA], [https://pdbe.org/2ypg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ypg RCSB], [https://www.ebi.ac.uk/pdbsum/2ypg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ypg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/HEMA_I68A0 HEMA_I68A0]] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.
+[https://www.uniprot.org/uniprot/HEMA_I68A0 HEMA_I68A0] Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization of about two third of the virus particles through clathrin-dependent endocytosis and about one third through a clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The hemagglutinin (HA) of influenza A(H3N2) virus responsible for the 1968 influenza pandemic derived from an avian virus. On introduction into humans, its receptor binding properties had changed from a preference for avian receptors (alpha2,3-linked sialic acid) to a preference for human receptors (alpha2,6-linked sialic acid). By 2001, the avidity of human H3 viruses for avian receptors had declined, and since then the affinity for human receptors has also decreased significantly. These changes in receptor binding, which correlate with increased difficulties in virus propagation in vitro and in antigenic analysis, have been assessed by virus hemagglutination of erythrocytes from different species and quantified by measuring virus binding to receptor analogs using surface biolayer interferometry. Crystal structures of HA-receptor analog complexes formed with HAs from viruses isolated in 2004 and 2005 reveal significant differences in the conformation of the 220-loop of HA1, relative to the 1968 structure, resulting in altered interactions between the HA and the receptor analog that explain the changes in receptor affinity. Site-specific mutagenesis shows the HA1 Asp-225--&gt;Asn substitution to be the key determinant of the decreased receptor binding in viruses circulating since 2005. Our results indicate that the evolution of human influenza A(H3N2) viruses since 1968 has produced a virus with a low propensity to bind human receptor analogs, and this loss of avidity correlates with the marked reduction in A(H3N2) virus disease impact in the last 10 y.
-Evolution of the receptor binding properties of the influenza A(H3N2) hemagglutinin.,Lin YP, Xiong X, Wharton SA, Martin SR, Coombs PJ, Vachieri SG, Christodoulou E, Walker PA, Liu J, Skehel JJ, Gamblin SJ, Hay AJ, Daniels RS, McCauley JW Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21474-9. doi:, 10.1073/pnas.1218841110. Epub 2012 Dec 10. PMID:23236176<ref>PMID:23236176</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2ypg" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Hemagglutinin 3D structures|Hemagglutinin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Christodoulou, E]]
+[[Category: Christodoulou E]]
-[[Category: Coombs, P J]]
+[[Category: Coombs PJ]]
-[[Category: Daniels, R S]]
+[[Category: Daniels RS]]
-[[Category: Gamblin, S J]]
+[[Category: Gamblin SJ]]
-[[Category: Haire, L F]]
+[[Category: Haire LF]]
-[[Category: Hay, A J]]
+[[Category: Hay AJ]]
-[[Category: Lin, Y P]]
+[[Category: Lin YP]]
-[[Category: Liu, J]]
+[[Category: Liu J]]
-[[Category: Martin, S R]]
+[[Category: Martin SR]]
-[[Category: McCauley, J W]]
+[[Category: McCauley JW]]
-[[Category: Skehel, J J]]
+[[Category: Skehel JJ]]
-[[Category: Vachieri, S G]]
+[[Category: Vachieri SG]]
-[[Category: Walker, P A]]
+[[Category: Walker PA]]
-[[Category: Wharton, S A]]
+[[Category: Wharton SA]]
-[[Category: Xiong, X]]
+[[Category: Xiong X]]
-[[Category: Glycoprotein]]
-[[Category: Influenza virus evolution]]
-[[Category: Membrane fusion]]
-[[Category: Receptor binding]]
-[[Category: Viral protein]]