3kbh: Difference between revisions

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 ==Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor==
-<StructureSection load='3kbh' size='340' side='right' caption='[[3kbh]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
+<StructureSection load='3kbh' size='340' side='right'caption='[[3kbh]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kbh]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_coronavirus_nl63 Human coronavirus nl63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KBH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KBH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kbh]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_coronavirus_NL63 Human coronavirus NL63]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KBH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KBH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 3.31&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ajf|2ajf]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ACE2, spike protein, UNQ868/PRO1885 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), 2, human angiotensin-converting enzyme 2, S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=277944 Human coronavirus NL63])</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=3kbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kbh OCA], [https://pdbe.org/3kbh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kbh RCSB], [https://www.ebi.ac.uk/pdbsum/3kbh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kbh 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=3kbh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kbh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kbh RCSB], [http://www.ebi.ac.uk/pdbsum/3kbh PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ACE2_HUMAN ACE2_HUMAN]] Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin-13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. In case of human coronaviruses SARS and HCoV-NL63 infections, serve as functional receptor for the spike glycoprotein of both coronaviruses.<ref>PMID:10969042</ref> <ref>PMID:10924499</ref> <ref>PMID:14647384</ref>  [[http://www.uniprot.org/uniprot/SPIKE_CVHNL SPIKE_CVHNL]] S1 region attaches the virion to the cell membrane by interacting with human ACE2, initiating the infection. Binding to the receptor probably induces conformational changes in the S glycoprotein unmasking the fusion peptide of S2 region and activating membranes fusion. S2 region belongs to the 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) regions 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 (By similarity).
+[https://www.uniprot.org/uniprot/ACE2_HUMAN ACE2_HUMAN] Carboxypeptidase which converts angiotensin I to angiotensin 1-9, a peptide of unknown function, and angiotensin II to angiotensin 1-7, a vasodilator. Also able to hydrolyze apelin-13 and dynorphin-13 with high efficiency. May be an important regulator of heart function. In case of human coronaviruses SARS and HCoV-NL63 infections, serve as functional receptor for the spike glycoprotein of both coronaviruses.<ref>PMID:10969042</ref> <ref>PMID:10924499</ref> <ref>PMID:14647384</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/kb/3kbh_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kb/3kbh_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3kbh ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3kbh" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Angiotensin-Converting Enzyme|Angiotensin-Converting Enzyme]]
+*[[Angiotensin-Converting Enzyme 3D structures|Angiotensin-Converting Enzyme 3D structures]]
+*[[Sandbox 3001|Sandbox 3001]]
+*[[Spike protein|Spike protein]]
+*[[Spike protein 3D structures|Spike protein 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 40: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Human coronavirus nl63]]
+[[Category: Human coronavirus NL63]]
-[[Category: Li, F]]
+[[Category: Large Structures]]
-[[Category: Li, W]]
+[[Category: Li F]]
-[[Category: Peng, G]]
+[[Category: Li W]]
-[[Category: Wu, K]]
+[[Category: Peng G]]
-[[Category: Beta sandwich]]
+[[Category: Wu K]]
-[[Category: Carboxypeptidase]]
-[[Category: Cell membrane]]
-[[Category: Chloride]]
-[[Category: Envelope protein]]
-[[Category: Fusion protein]]
-[[Category: Glycoprotein]]
-[[Category: Host-virus interaction]]
-[[Category: Hydrolase]]
-[[Category: Membrane]]
-[[Category: Metal-binding]]
-[[Category: Metalloprotease]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Transmembrane]]
-[[Category: Virion]]
-[[Category: Virulence]]