5uk2: Difference between revisions

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-'''Unreleased structure'''
-The entry 5uk2 is ON HOLD
+==CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 4==
+<SX load='5uk2' size='340' side='right' viewer='molstar' caption='[[5uk2]], [[Resolution|resolution]] 4.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5uk2]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Solomon_Islands/3/2006(H1N1)) Influenza A virus (A/Solomon Islands/3/2006(H1N1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UK2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UK2 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5uk2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uk2 OCA], [https://pdbe.org/5uk2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uk2 RCSB], [https://www.ebi.ac.uk/pdbsum/5uk2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uk2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A7UPX0_9INFA A7UPX0_9INFA] 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.[RuleBase:RU003324][SAAS:SAAS00145386]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structure-based vaccine design depends on extensive structural analyses of antigen-antibody complexes.Single-particle electron cryomicroscopy (cryoEM) can circumvent some of the problems of x-ray crystallography as a pipeline for obtaining the required structures. We have examined the potential of single-particle cryoEM for determining the structure of influenza-virus hemagglutinin (HA):single-chain variable-domain fragment complexes, by studying a complex we failed to crystallize in pursuing an extended project on the human immune response to influenza vaccines.The result shows that a combination of cryoEM and molecular modeling can yield details of the antigen-antibody interface, although small variation in the twist of the rod-likeHA trimer limited the overall resolution to about 4.5A.Comparison of principal 3D classes suggests ways to modify the HA trimer to overcome this limitation. A closely related antibody from the same donor did yield crystals when bound with the same HA, giving us an independent validation of the cryoEM results.The two structures also augment our understanding of receptor-binding site recognition by antibodies that neutralize a wide range of influenza-virus variants.
-Authors: Liu, Y., Pan, J., Caradonna, T., Jenni, S., Rayond, D.D., Schmidt, A.G., Harrison, S.C., Grigorieff, N.
+CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface.,Liu Y, Pan J, Jenni S, Raymond DD, Caradonna T, Do KT, Schmidt AG, Harrison SC, Grigorieff N J Mol Biol. 2017 Jun 16;429(12):1829-1839. doi: 10.1016/j.jmb.2017.05.011. Epub, 2017 May 12. PMID:28506635<ref>PMID:28506635</ref>
-Description: CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface -Class 4
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Rayond, D.D]]
+<div class="pdbe-citations 5uk2" style="background-color:#fffaf0;"></div>
-[[Category: Liu, Y]]
-[[Category: Grigorieff, N]]
+==See Also==
-[[Category: Schmidt, A.G]]
+*[[Antibody 3D structures|Antibody 3D structures]]
-[[Category: Harrison, S.C]]
+*[[Hemagglutinin 3D structures|Hemagglutinin 3D structures]]
-[[Category: Jenni, S]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-[[Category: Pan, J]]
+*[[3D structures of human antibody|3D structures of human antibody]]
-[[Category: Caradonna, T]]
+== References ==
+<references/>
+__TOC__
+</SX>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Caradonna T]]
+[[Category: Grigorieff N]]
+[[Category: Harrison SC]]
+[[Category: Jenni S]]
+[[Category: Liu Y]]
+[[Category: Pan J]]
+[[Category: Raymond DD]]
+[[Category: Schmidt AG]]