4xak: Difference between revisions

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 ==Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD==
-<StructureSection load='4xak' size='340' side='right' caption='[[4xak]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+<StructureSection load='4xak' size='340' side='right'caption='[[4xak]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xak]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Betacoronavirus_england_1 Betacoronavirus england 1] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XAK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xak]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Betacoronavirus_England_1 Betacoronavirus England 1] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XAK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.45&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">S, 3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1263720 Betacoronavirus England 1])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xak OCA], [http://pdbe.org/4xak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xak RCSB], [http://www.ebi.ac.uk/pdbsum/4xak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xak 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=4xak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xak OCA], [https://pdbe.org/4xak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xak RCSB], [https://www.ebi.ac.uk/pdbsum/4xak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xak ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SPIKE_CVEMC SPIKE_CVEMC]] S1 attaches the virion to the cell membrane by interacting with host DPP4, initiating the infection.<ref>PMID:23486063</ref>   S2 is a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and plasma cell membranes (By similarity).
+[https://www.uniprot.org/uniprot/SPIKE_MERS1 SPIKE_MERS1] Attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Interacts with host DPP4 to mediate virla entry.[HAMAP-Rule:MF_04099]<ref>PMID:23486063</ref>   Mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099]  Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 21: @@
 ==See Also==
-*[[3D structures of antibody|3D structures of antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Sandbox 3001|Sandbox 3001]]
+*[[Spike protein 3D structures|Spike protein 3D structures]]
+*[[3D structures of human antibody|3D structures of human antibody]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Betacoronavirus england 1]]
+[[Category: Betacoronavirus England 1]]
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Dimtrov, D S]]
+[[Category: Large Structures]]
-[[Category: Ying, T]]
+[[Category: Dimtrov DS]]
-[[Category: Zhou, T]]
+[[Category: Ying T]]
-[[Category: Antibody m336]]
+[[Category: Zhou T]]
-[[Category: Immune system]]
-[[Category: Mers-cov rbd]]
-[[Category: Neutralization]]