PDB-101: Molecule of the Month: SARS-CoV-2 Spike

<!DOCTYPE html> <html> <head> <script src="https://www.googletagmanager.com/gtag/js?id=G-EPQ9202NVY" async></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); //- gtag('config', 'UA-71059016-1'); gtag('config', 'G-EPQ9202NVY'); </script> <title>PDB-101: Molecule of the Month: SARS-CoV-2 Spike</title> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1"> <meta property="og:title" content="PDB101: Molecule of the Month: SARS-CoV-2 Spike"> <meta property="og:description" content="Coronavirus spike protein binds to receptors on cell surfaces, and is a target for vaccine development."> <meta property="og:image" content="https://cdn.rcsb.org/pdb101/motm/246/246-SARSCoV2_Spike-6crz_6vxx3.jpg"> <meta property="og:url" content="http://pdb101.rcsb.org/motm/246"> <meta property="og:site_name" content="RCSB: PDB-101"> <meta 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overflow-wrap: break-word; } div.jmol-image { margin-bottom: 5px; } </style> <script> // jmol script var jmolLoaded = false function loadIframe() { if (jmolLoaded == false) { var src = '/motm/jmol/?id=' + 246 console.log('src=' + src) $("#iframe").attr('src', src) jmolLoaded = true } } function clickJmolTab() { $('#jmol-tab').trigger('click') } // jmol script for legacy motms with multiple jmols var jmols = []; function loadIframeById(jmolId) { var jmol = jmols[jmolId - 1] if (jmol.loaded == false) { var src = '/motm/jmol/?id=' + 246 + '&jmolId=' + jmolId $("#iframe_" + jmolId).attr('src', src) jmol.loaded = true } } function clickJmolTab(i) { var j = i + 1 $('#jmol-tab-' + j).trigger('click') } </script> <div id="sub-navbar"> <div class="row hidden-print"> <div class="col-xs-12 col-sm-6 sub-navbar"> <h4>Molecule of the Month</h4> </div> <div class="col-xs-12 col-sm-6 text-right sub-navbar"> <table> <tr> <td onclick="location.href="/motm/motm-by-category"">By Category</td> <td onclick="location.href="/motm/motm-by-date"">By Date</td> <td onclick="location.href="/motm/motm-by-title"">By Title</td> </tr> </table> </div> </div> </div> <div data-elastic-include> <h1>Molecule of the Month: SARS-CoV-2 Spike</h1> <p><i>Coronavirus spike protein binds to receptors on cell surfaces, and is a target for vaccine development.</i></p> <div> <div class="img-with-caption float-right"> <div class="img-with-caption-table"><img src="https://cdn.rcsb.org/pdb101/motm/246/246-SARSCoV2_Spike-6crz_6vxx3.jpg" alt="Spike protein from SARS-CoV, with one receptor binding domain (RBD) in the up position, and a closed conformation of the SARS-CoV-2 spike. The S1 fragment is shown in magenta and the S2 fragment in red, with glycosylation in lighter shades." class="img-responsive"> <div class="img-caption"> <div style="margin-bottom:10px;"><i>Spike protein from SARS-CoV, with one receptor binding domain (RBD) in the up position, and a closed conformation of the SARS-CoV-2 spike. The S1 fragment is shown in magenta and the S2 fragment in red, with glycosylation in lighter shades.</i></div><a href="https://cdn.rcsb.org/pdb101/motm/246/246-SARSCoV2_Spike-6crz_6vxx3.tif"><small>Download high quality TIFF image<span class="fa fa-cloud-download"></span></small></a> </div> </div> </div> <div>The research community has quickly mobilized to fight the current SARS-CoV-2 pandemic, building on years of work on the previous SARS-CoV virus. The spike protein of this virus will be a central figure in this fight, since it is the primary target of antibodies that provide immunity against the virus. The surfaces of coronaviruses are covered with these spikes, giving them their distinctive crown-like appearance in electron micrographs. The spikes initiate the process of infection, binding to receptors and then fusing with the cell membrane to release the viral genome inside. Many other enveloped viruses use similar spike-like proteins to infect cells, including <a href='/motm/76'>influenza hemagglutinin</a>, and the envelope glycoproteins of <a href='/motm/169'>HIV-1</a> and <a href='/motm/178'>ebola</a>.</div> <h4>Cut to Size</h4> <div>The spike protein is composed of three identical chains, that together form a complex with a small domain inside the virus, a membrane-spanning segment, and a large ectodomain that extends outward from the virus. In addition, the spike is a glycoprotein: the ectodomain is covered with sugar chains that help to mask the virus from the immune system. The structures of SARS-CoV and SARS-COV-2 spikes shown here (PDB entries <a href='https://www.rcsb.org/structure/6crz' target='_blank'>6crz</a> and <a href='https://www.rcsb.org/structure/6vxx' target='_blank'>6vxx</a>) include only the ectodomain, and as you can see, they are very similar. Each chain is synthesized in one piece, but then is clipped by cellular proteases into two functional pieces. The outer S1 fragment, colored magenta, binds to cellular receptors, and the S2 fragment, colored red, directs fusion of the virus with the cell. Both of these structures include only portions of the many sugar chains that coat the spike, since the sugars are highly flexible and difficult to observe.</div> <h4>Flexible Features</h4> <div>Recent structures have revealed that the spikes of SARS-CoV and SARS-CoV-2 are quite flexible. In these structures, the receptor-binding domains are seen in different conformations. Often, just one domain is extended upwards, but sometimes they're all tucked down or several are extended. The extended conformation is needed to bind to receptors, so this flexibility is a great advantage to the virus. Researchers hypothesize that the recent SARS variants are virulent because their receptor binding domains are particularly flexible, whereas the more widespread coronaviruses that cause the common cold are less dangerous because they are less flexible.</div> </div> <div class="clearfix"></div> <hr class="motm-hr"> <div> <div class="img-with-caption float-left"> <div class="img-with-caption-table"><img src="https://cdn.rcsb.org/pdb101/motm/246/246-Coronavirus_Spike-6vsb_6m17_2.jpg" alt="Illustration of a complex of the spike protein (red and magenta) bound to its receptor ACE2 (blue). ACE2 is part of a complex with the amino acid transporter B0AT1 (green). The cell membrane is shown schematically in light blue at the bottom." class="img-responsive"> <div class="img-caption"> <div style="margin-bottom:10px;"><i>Illustration of a complex of the spike protein (red and magenta) bound to its receptor ACE2 (blue). ACE2 is part of a complex with the amino acid transporter B0AT1 (green). The cell membrane is shown schematically in light blue at the bottom.</i></div><a href="https://cdn.rcsb.org/pdb101/motm/246/246-Coronavirus_Spike-6vsb_6m17_2.tif"><small>Download high quality TIFF image<span class="fa fa-cloud-download"></span></small></a> </div> </div> </div> <h4>Receptor Binding</h4> <div>Spike protein binds to ACE2 (angiotensin-converting enzyme 2) on the surface of cells. ACE2 is an enzyme that activates angiotensin, a peptide hormone involved in control of blood pressure. ACE2 is found on lung, heart, kidney, and intestinal cells, making these cells the target for infection by the virus. PDB entry <a href='https://www.rcsb.org/structure/6m17' target='_blank'>6m17</a> reveals the complex of ACE2 with the receptor-binding domain of the SARS-CoV-2 spike. In the complex, ACE2 is also bound to the amino acid transporter B0AT1. The illustration was created by superimposing this complex with the structure of the spike protein in PDB entry <a href='https://www.rcsb.org/structure/6vsb' target='_blank'>6vsb</a>.</div> </div> <div class="clearfix"></div> <hr class="motm-hr"> <h4>Exploring the Structure</h4> <div id="jmolTabs" class="jmolText"> <ul class="nav nav-tabs"> <li class="active"><a data-toggle="tab" href="#tabs-1">Image</a></li> <li><a id="jmol-tab" data-toggle="tab" href="#tabs-2" onclick="loadIframe();">JSmol</a></li> </ul> <div class="tab-content"> <div id="tabs-1" class="tab-pane active"> <h5>Antibodies bound to the spike receptor-binding domain</h5> <div style="margin-top:0;" class="img-with-caption float-left"><img src="https://cdn.rcsb.org/pdb101/motm/246/246-Coronavirus_Spike-RBD_jmol.jpg" onclick="clickJmolTab();" class="img-responsive"></div> <p>Our immune system fights back when coronaviruses infect us. The spike is the major target for this protection, since it is exposed on the surface of the virus. These three structures (PDB entries <a href='https://www.rcsb.org/structure/3bgf' target='_blank'>3bgf</a>, <a href='https://www.rcsb.org/structure/2ghw' target='_blank'>2ghw</a> and <a href='https://www.rcsb.org/structure/6w41' target='_blank'>6w41</a> show that antibodies (shown in green) can recognize spike proteins in many ways. Two of these antibodies block the receptor-binding portion of the domain (shown here in brighter colors), but the other antibody targets a cryptic site at the base of the domain, that is only exposed when the antibody binds to it. To explore these structures in more detail, click on the image for an interactive JSmol.</p> <div class="clearfix"></div> </div> <div id="tabs-2" class="tab-pane"> <iframe id="iframe" marginheight="0" marginwidth="0" scrolling="yes" frameborder="0" width="100%"></iframe> </div> </div> </div> <div class="row"> <div class="col-xs-12 col-sm-12 col-md-6"> <h4>Topics for Further Discussion</h4> <ol> <li>For more information on SARS-CoV-2 and COVID-19, visit the resource pages at the <a href="http://RCSB.org/covid19">main RCSB PDB site</a> and at <a href="http://pdb101.rcsb.org/browse/coronavirus">PDB-101</a>.</li> </ol> <div data-elastic-exclude> <div class="col-xs-12 link-motm"> <h4>Related PDB-101 Resources</h4> <ul> <li>Browse <a href="/browse/coronavirus">Coronavirus</a></li> <li>Browse <a href="/browse/viruses">Viruses</a></li> <li>Browse <a href="/browse/vaccines">Vaccines</a></li> </ul> </div> </div> </div> <div style="border-left:1px dashed #ddd;" class="col-xs-12 col-sm-12 col-md-6"> <h4>References</h4> <ol> <li>6vxx: Walls, A.C.,聽Park, Y.J.,聽Tortorici, M.A.,聽Wall, A.,聽McGuire, A.T.,聽Veesler, D. (2020) Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell聽181, 281-292</li> <li>6w41: Yuan, M.,聽Wu, N.C.,聽Zhu, X.,聽Lee, C.D.,聽So, R.T.Y.,聽Lv, H.,聽Mok, C.K.P.,聽Wilson, I.A. (2020) A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science聽DOI: 10.1126/science.abb7269</li> <li>6vsb: Wrapp, D.,聽Wang, N.,聽Corbett, K.S.,聽Goldsmith, J.A.,聽Hsieh, C.L.,聽Abiona, O.,聽Graham, B.S.,聽McLellan, J.S. (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science聽367: 1260-1263</li> <li>6m17: Yan, R.,聽Zhang, Y.,聽Li, Y.,聽Xia, L.,聽Guo, Y.,聽Zhou, Q. (2020) Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science聽367: 1444-1448</li> <li>6crz: Kirchdoerfer, R.N.,聽Wang, N.,聽Pallesen, J.,聽Wrapp, D.,聽Turner, H.L.,聽Cottrell, C.A.,聽Corbett, K.S.,聽Graham, B.S.,聽McLellan, J.S.,聽Ward, A.B. (2018) Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis. Sci Rep聽8: 15701-15701</li> <li>3bgf: Pak, J.E.,聽Sharon, C.,聽Satkunarajah, M.,聽Auperin, T.C.,聽Cameron, C.M.,聽Kelvin, D.J.,聽Seetharaman, J.,聽Cochrane, A.,聽Plummer, F.A.,聽Berry, J.D.,聽Rini, J.M. (2009) Structural insights into immune recognition of the severe acute respiratory syndrome coronavirus S protein receptor binding domain. J Mol Biol聽388: 815-823</li> <li>2ghw: Hwang, W.C.,聽Lin, Y.,聽Santelli, E.,聽Sui, J.,聽Jaroszewski, L.,聽Stec, B.,聽Farzan, M.,聽Marasco, W.A.,聽Liddington, R.C. (2006) Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R. J Biol Chem聽281: 34610-34616</li> </ol> </div> </div> <hr class="motm-hr"> <p>June 2020, David Goodsell</p> <a href="http://doi.org/10.2210/rcsb_pdb/mom_2020_6">http://doi.org/10.2210/rcsb_pdb/mom_2020_6</a> </div> <div style="margin-top:20px;" class="row hidden-print"> <div class="col-xs-12"> <div class="panel panel-info"> <div class="panel-heading">About Molecule of the Month</div> <div class="panel-body"><small> The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.<a href="/motm/motm-about">More</a></small> </div> </div> </div> </div> <script> $('#iframe').load(function () { $(this).height($(this).contents().find('body').height() + 30); }); </script> </div> <div id="footer_main" class="hidden-print"> <div class="container"> <div class="row"> <div class="col-sm-12 col-md-7"> <p><strong>About PDB-101</strong></p> <p>Researchers around the globe make 3D structures freely available from the Protein Data Bank (PDB) archive. PDB-101 training materials help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. 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PDB-101: Molecule of the Month: SARS-CoV-2 Spike