PDB-101: Molecule of the Month: Adenine Riboswitch in Action

<!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: Adenine Riboswitch in Action</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: Adenine Riboswitch in Action"> <meta property="og:description" content="XFEL serial crystallography reveals what happens when adenine binds to a riboswitch"> <meta property="og:image" content="https://cdn.rcsb.org/pdb101/motm/210/210-Adenine_Riboswitch_in_Action-5e54_5swe.jpg"> <meta property="og:url" content="http://pdb101.rcsb.org/motm/210"> <meta property="og:site_name" content="RCSB: 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'/motm/jmol/?id=' + 210 + '&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: Adenine Riboswitch in Action</h1> <p><i>XFEL serial crystallography reveals what happens when adenine binds to a riboswitch</i></p> <div> <div class="img-with-caption float-right"> <div class="img-with-caption-table"><img src="https://cdn.rcsb.org/pdb101/motm/210/210-Adenine_Riboswitch_in_Action-5e54_5swe.jpg" alt="Adenine riboswitch aptamer domain before binding of adenine (left) and with adenine (right). The “latch” region (yellow) undergoes a large change to accommodate binding of adenine, and the “stem” region (red) forms a stable double helix." class="img-responsive"> <div class="img-caption"> <div style="margin-bottom:10px;"><i>Adenine riboswitch aptamer domain before binding of adenine (left) and with adenine (right). The “latch” region (yellow) undergoes a large change to accommodate binding of adenine, and the “stem” region (red) forms a stable double helix.</i></div><a href="https://cdn.rcsb.org/pdb101/motm/210/210-Adenine_Riboswitch_in_Action-5e54_5swe.tif"><small>Download high quality TIFF image<span class="fa fa-cloud-download"></span></small></a> </div> </div> </div> <div><a href='/motm/130'>Riboswitches</a> are structurally dynamic RNA molecules, undergoing changes in shape as they perform their regulatory functions. Riboswitches typically have two domains: a ligand-binding “aptamer” domain that changes conformation when it binds to a specific ligand, which then sends a signal to an “expression platform” domain that regulates use of the RNA. Thus far, structures have been obtained for the aptamer domains, but the motions caused by ligand binding have been tricky to observe by crystallography: crystals typically freeze molecules in one shape, so crystallographic structures of unbound aptamers typically look very similar to the ligand-bound form. Researchers are using XFEL radiation sources in a clever way to help surmount this limitation and observe directly what happens when a ligand binds.</div> <h4>Free Electron Lasers</h4> <div>Free electron lasers (FEL) provide very bright, but very short, pulses of X-rays. In XFEL experiments, a stream of very tiny crystals is flowed past the beam, and each time a crystal is caught in one of the pulses, it creates an instantaneous diffraction pattern that captures the molecules in the crystal at a defined moment of time. By collecting similar diffraction patterns from many crystals caught in random orientations by the X-ray beam, researchers build up a full diffraction data set.</div> <h4>Mix-and-Inject</h4> <div>To capture the dynamics of molecules, researchers start a reaction and then collect diffraction patterns at a given time after the reaction starts. In studies of <a href='/motm/207'>photoactive yellow protein</a>, researchers flash the crystals with light and then watch what happens. For example, in the case of riboswitches, researchers add the specific signaling molecule, in this case, adenine. Two structures are shown here. The first shows the riboswitch without adenine (PDB entry <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=5e54' target='_blank'>5e54</a>). For the second, researchers mixed the crystals with adenine, waited 10 minutes, then gathered XFEL data. The adenine-bound form shows a large change in conformation that creates a stable double helix at the end of the riboswitch (PDB entry <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=5swe' target='_blank'>5swe</a>).</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/210/210-Adenine_Riboswitch_in_Action-5e54_5swe_lattice.jpg" alt="Crystal lattice of the adenine riboswitch aptamer before binding of adenine (top) and with adenine (bottom)." class="img-responsive"> <div class="img-caption"> <div style="margin-bottom:10px;"><i>Crystal lattice of the adenine riboswitch aptamer before binding of adenine (top) and with adenine (bottom).</i></div><a href="https://cdn.rcsb.org/pdb101/motm/210/210-Adenine_Riboswitch_in_Action-5e54_5swe_lattice.tif"><small>Download high quality TIFF image<span class="fa fa-cloud-download"></span></small></a> </div> </div> </div> <h4>Dynamic Crystals</h4> <div>Biomolecular crystals often have large channels of solvent between the molecules, so ligands may be soaked into the crystal to explore their binding. Unfortunately changes this large are rarely observed by conventional crystallography because larger crystals are needed to collect data using synchotron X-ray sources, and the larger crystals often crack when the ligand binds. This study of riboswitches, however, demonstrates that the tiny crystals used for XFEL are able to rearrange to accommodate large molecular motions. The crystal lattices for the unbound and bound forms are shown here—notice that the large change in shape forces the aptamers to pack in an entirely different way.</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>Adenine Riboswitch</h5> <div style="margin-top:0;" class="img-with-caption float-left"><img src="https://cdn.rcsb.org/pdb101/motm/210/210-Adenine_Riboswitch_in_Action-5swd_JSmol.jpg" onclick="clickJmolTab();" class="img-responsive"></div> <p>In this XFEL study, a structure was also captured 10 seconds after addition of adenine, revealing an intermediate state with adenine in the binding pocket, but before the stem and latch regions had a chance to rearrange into the stable bound conformation (PDB entry <a href='http://www.rcsb.org/pdb/explore/explore.do?structureId=5swd' target='_blank'>5swd</a>). You can explore all of these structures in the interactive JSMol using the button above the image.</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>XFEL is a new technique, but there are already many structures in the PDB archive determined with the method. Try searching for “XFEL” to see some of them.</li> <li>Structures of dozens of different types of riboswitches have been determined—search for “riboswitch” to see them.</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/biomolecules">Biomolecules</a></li> <li>Browse <a href="/browse/protein-synthesis">Protein Synthesis</a></li> <li>Browse <a href="/browse/biomolecular-structural-biology">Biomolecular Structural Biology</a></li> <li>Browse <a href="/browse/nucleic-acids">Nucleic Acids</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>CP Jones & AR Ferré-D’Amaré (2017) Long-range interactions in riboswitch control of gene expression. Annual Review of Biophysics 46, 455-481.</li> <li>5e54, 5swd, 5swe. JR Stagno, Y Liu, YR Bhandari, CE Conrad, S Panja, M Swain, L Fan, G Nelson, C Li, DR Wendel, TA White, JD Coe, MO Wiedorn, J Knoska, D Oberthuer, RA Tuckey, P Yu, M Dyba, SG Tarasov, U Weierstall, TD Grant, CD Schwieters, J Zhang, AR Ferré-D’Amaré, P Fromme, DE Draper, M Liang, MS Hunter, S Boutet, K Tan, X Zuo, X Ji, A Barty, NA Zatsepin, H N Chapman, JCH Spence, SA Woodson & YX Wang (2017) Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541, 242-246.</li> </ol> </div> </div> <hr class="motm-hr"> <p>June 2017, David Goodsell</p> <a href="http://doi.org/10.2210/rcsb_pdb/mom_2017_6">http://doi.org/10.2210/rcsb_pdb/mom_2017_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-6"> <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. Outreach content demonstrate how PDB data impact fundamental biology, biomedicine, bioengineering/biotechnology, and energy sciences in 3D for a diverse and multidisciplinary user community. Education Materials provide lessons and activities for teaching and learning.</p> <p>PDB-101 is developed by the <a href="https://rcsb.org" target="_blank">RCSB PDB</a>.</p> </div> <div class="col-sm-12 col-md-6 text-center"> <p>RCSB PDB (<a href="http://nar.oxfordjournals.org/content/28/1/235.abstract" target="blank">citation</a>) is hosted by</p> <p><img src="https://cdn.rcsb.org/rcsb-pdb//v2/common/images/rad-sm.png" alt="Rutgers RAD logo.png" usemap="#rutgers-map" height="34" style="padding:0px 10px; border-right: 1px solid #666;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSD-SDSC.png" alt="Logo_UCSD.png" usemap="#UCSD-SDSC-map" height="26" style="padding: 0px 10px; border-right: 1px solid #666;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSF.png" alt="Logo_UCSF.png" usemap="#UCSF-map" height="26" style="padding-left: 10px;"><map name="rutgers-map"> <area shape="rect" coords="0,0,115,26" href="https://radcollaboratory.rutgers.edu/" alt="Rutgers-RAD" target="_blank"></map><map name="UCSD-SDSC-map"> <area shape="rect" coords="0,0,150,26" href="http://ucsd.edu/" alt="UCSD" target="_blank"> <area shape="rect" coords="151,0,255,26" href="http://www.sdsc.edu/" alt="SDSC" target="_blank"></map><map name="UCSF-map"> <area shape="rect" coords="0,0,64,26" href="http://www.ucsf.edu/" alt="UCSF" target="_blank"></map></p><br> <p>RCSB PDB is a member of </p> <p><span id='pdbmembers_footer'><a href='http://www.wwpdb.org/' target='_blank'><img src='//cdn.rcsb.org/pdb101/common/images/Logo_wwpdb.png' width='70'></a><span class='pipe'></span><a href='http://www.emdatabank.org/' target='_blank'><img src='https://cdn.rcsb.org/pdb101/common/images/EMDataResourcelogo.png' width='100'></a></p> </div> </div> </div> </div> <div id="footer_grant" class="hidden-print"> <div class="container"> <div class="row"> <p>RCSB PDB Core Operations are funded by the <a href="http://www.nsf.gov/" target="_blank">U.S. National Science Foundation</a> (DBI-2321666), the <a href="http://science.energy.gov/" target="_blank">US Department of Energy</a> (DE-SC0019749), and the <a href="http://www.cancer.gov/" target="_blank">National Cancer Institute</a>, <a href="http://www.niaid.nih.gov/" target="_blank">National Institute of Allergy and Infectious Diseases</a>, and <a href="http://www.nigms.nih.gov/" target="_blank">National Institute of General Medical Sciences</a> of the <a href="http://www.nih.gov/" target="_blank">National Institutes of Health</a> under grant R01GM157729.</p> </div> </div> </div> <div id="jira-fdbck"></div><script> //Google Analytics tracking code {/* (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-71059016-1', 'auto'); ga('send', 'pageview'); */} </script> </div> </body> </html>

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PDB-101: Molecule of the Month: Adenine Riboswitch in Action