CINXE.COM

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>wwPDB Deposition & Annotation System Now Available for 3DEM Structures</title> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">  <script async src="https://www.googletagmanager.com/gtag/js?id=G-0N32KDVZDG"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-0N32KDVZDG'); </script> <meta property="og:title" content="EMDataResource" /> <meta property="og:type" content="website" /> <meta property="og:url" content="https://www.emdataresource.org" /> <meta property="og:image" content="/images/EMDataResource-logo-small.png" /> <link rel="shortcut icon" href="/favicon.ico"> <link href="/css/bootstrap4.1.3.min.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <link href="/css/em-styles-cutdown.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <link href="/css/navbar.css" type="text/css" rel="stylesheet" media="screen, projection, print"/> <script src="/js/jquery-3.3.1.min.js" type="text/javascript"></script> <script src="/js/popper1.12.9.min.js" type="text/javascript"></script> <script src="/js/bootstrap4.1.3.min.js" type="text/javascript"></script> <script type="text/javascript" src="/js/bootstrap3-typeahead.min.js"></script> </head> <body> <div class="container"> <div class="card" style="border: none; margin-bottom: 0px;" > <div class="card-header clearfix" style="background-color: #CCC;"> <div class="float-left"><b><span id="siteid"></span></b></div> <script> var sitebanner="" if (location.hostname.search("test") != -1) {sitebanner = "PRE-PRODUCTION STAGING SITE"; } if (location.hostname.search("159.51") != -1) {sitebanner = "PRE-PRODUCTION STAGING SITE"; } else if (location.hostname.search("dev") != -1) {sitebanner = "DEVELOPMENT SITE"; } else if (location.hostname.search("beta") != -1) {sitebanner = "BETA TESTING SITE"; } else if (location.hostname.search("4.80") != -1) {sitebanner = "REVIEW SITE"; } document.getElementById("siteid").innerHTML = sitebanner; </script> <div class="float-right"><span id="update_date">2025-02-12</span> : <span id="map_entries">42644</span> EMDB map entries, <span id="coordinate_entries">24982 PDB coordinate entries <a href="https://go.rutgers.edu/zcuqsog5" target="_blank">RCSB PDB</a> | <a href="https://go.rutgers.edu/paqlf60v" target="_blank" >PDBe</a> </span>  </div> </div> <div class="card-body" style="padding: 2px 15px;" > <div class="float-left"><a href="/index.html"> <img src="/images/EMDataResource-logo-small.png" alt="EMDataResource.org" height="78" style="margin-right: 25px;" /> </a></div> </div> <nav class="navbar navbar-expand-lg navbar-dark"> <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div class="collapse navbar-collapse" id="navbarSupportedContent"> <ul class="nav navbar-nav mr-auto"> <li class="nav-item"> <a class="nav-link" href="/index.html">Home</a></li> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> About</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/mission.html">Mission</a> <a class="dropdown-item" href="/team.html">Team</a> <a class="dropdown-item" href="/dictionaries.html">Dictionaries</a> <a class="dropdown-item" href="/conventions.html">Conventions</a> <a class="dropdown-item" href="/validation.html">Validation</a> <a class="dropdown-item" href="/project_publications.html">Publications</a> <a class="dropdown-item" href="/funding.html">Funding</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/deposit.html">Deposit</a></li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Search</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/emdlist=all">EMDR Search</a> <a class="dropdown-item" href="/coronavirus_search.html">CoV Enhanced Search</a> <a class="dropdown-item" href="/solrfacet.html">EMDR Search Term Facet Tool</a> <a class="dropdown-item" href="/searchnonrel.html">Search Proc/Hold/Obs/Wdrn Entries</a> <a class="dropdown-item" href="/search.html">All EMDB Search Options</a> </div> </li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Tools</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/statistics.html">Statistics</a> <a class="dropdown-item" href="https://ptp.emdataresource.org">RNA Virtual Torsion Analysis</a> <a class="dropdown-item" href="/emsoftware.html">EM Software List</a> <a class="dropdown-item" href="/emtestdata.html">3DEM Test Data</a> <a class="dropdown-item" href="/emdbaccess.html">EMDB Access</a> </div> </li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Archive</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown">  <a class="dropdown-item" href="/challenges/index.html">EMDR Challenges</a> <a class="dropdown-item" href="/workshops.html">Workshops</a> <a class="dropdown-item" href="/emdbac.html">Advisory Committee</a> </div> </li> <li class="nav-item"><a class="nav-link" href="/allnews.html">News</a></li> <li class="nav-item"><a class="nav-link" href="/externallinks.html">Links</a></li> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Help</a> <div class="dropdown-menu" aria-labelledby="navbarDropdown"> <a class="dropdown-item" href="/contactus.html">Contact Us</a> <a class="dropdown-item" href="/faq.html">FAQ</a> </div> </li> </ul> <form class="form-inline my-2 my-lg-0"> <input id="homequery" class="form-control typeahead mr-sm-2" data-sho-hint-on-focus="true" data-provide="typeahead" autocomplete="off" data-autoselect="false" type="search" placeholder="Search EMDB" aria-label="Search EMDB"> <button id="btnSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" style="background-color: #CCC;" ><img src="/images/search_icon.svg" alt="search" /></button> </form> </div> </nav> <div class="card-body"> <h2>wwPDB Deposition & Annotation System Now Available for 3DEM Structures</h2> <p>The wwPDB partners and the Unified Data Resource project are pleased to announce the launch of a new Deposition & Annotation system that supports structures determined using 3DEM, NMR, and X-ray, neutron and electron crystallography. New entries can be submitted at <a href="http://deposit.wwpdb.org/deposition/" target="_blank">http://deposit.wwpdb.org/deposition/</a>. </p> <p>This new system interoperates with EMDB and BMRB to enable joint depositions of both atomic coordinates (PDB) and EM electron-density maps (EMDB) or NMR experimental data (BMRB). PDB, EMDB and BMRB accession codes will be issued as appropriate immediately after a structure has been deposited. </p> <p>A brief tutorial is available at <a href="http://www.wwpdb.org/deposition/tutorial" target="_blank">http://www.wwpdb.org/deposition/tutorial</a>.</p> <p>In January 2014, the wwPDB launched the Deposition & Annotation system for structures determined using X-ray crystallography in the first phase of our roll-out of a single global system for deposition and annotation of structural data. Using this system, more than 12,000 X-ray structures have been deposited and annotated, and more than 6,800 entries released in the PDB archive.</p> <p>New or enhanced features of the global combined X-ray/3DEM/NMR wwPDB Deposition & Annotation system include generation and review of validation reports that follow <a href="http://www.wwpdb.org/task/validation-task-forces" target="_blank">wwPDB Task Force</a> recommendations,1,2,3 improved capture and review of ligand information, replacement of atomic coordinate and/or experimental data files both pre- and post-submission, and improved communication between depositors and wwPDB curators.</p> <p>In addition to the new system, depositors will continue to have the option of using one of the legacy deposition tools (EMDep, ADIT-NMR, AutoDep) to start a new deposition for at least the first half of 2016. </p> <p>Once the new system is deemed stable, the legacy deposition tools will be phased out with sufficient time allowed for completion of in-progress sessions. This process mirrors the one used in early 2015 for successful shutdown of the legacy ADIT system supporting deposition of X-ray structures.</p> <ol> <li> A New Generation of Crystallographic Validation Tools for the Protein Data Bank, Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas L眉tteke, Zbyszek Otwinowski, Anastassis Perrakis, Jane S. Richardson, William H. Sheffler, Janet L. Smith, Ian J. Tickle, Gert Vriend and Peter H. Zwart. (2011) Structure 19: 1395-1412 doi: <a href="http://dx.doi.org/10.1016/j.str.2011.08.006" target="_blank">10.1016/j.str.2011.08.006</a> </li> <li> Outcome of the First Electron Microscopy Validation Task Force Meeting, Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schr枚der, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson. (2012) Structure 20: 205-214 doi:<a href="http://dx.doi.org/10.1016/j.str.2011.12.014" target="_blank">10.1016/j.str.2011.12.014</a> </li> <li> Recommendations of the wwPDB NMR Validation Task Force, Gaetano T. Montelione, Michael Nilges, Ad Bax, Peter G眉ntert, Torsten Herrmann, Jane S. Richardson, Charles D. Schwieters, Wim F. Vranken, Geerten W. Vuister, David S. Wishart, Helen M. Berman, Gerard J. Kleywegt, and John L. Markley. (2013) Structure 21: 1563-1570 doi:<a href="http://dx.doi.org/10.1016/j.str.2013.07.021" target="_blank">10.1016/j.str.2013.07.021</a> </li> </ol> <br /> Source: <a href="http://wwpdb.org/news/news?year=2016#11-January-2016" target="_blank" >wwPDB News</a> <br class="clearfloat" /> </div> <br class="clearfloat" /> <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="color:#666; background-color: #E4E4E4; padding-top: 18px; padding-bottom: 3px;"> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://cryoem.slac.stanford.edu" target="_blank"> <img src="/images/ncmi-logo.png" alt="Stanford-CryoEM" height="35px"/></a> </div> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://www.rcsb.org" target="_blank"> <img src="/images/rcsb-pdb-logo.png" alt="PDB" height="35px"/></a> </div> <div class="col-sm-2" style="padding-top: 10px; padding-bottom: 10px;"> <a href="https://www.ebi.ac.uk/emdb/" target="_blank"> <img src="/images/EMDB_logo_2017.png" alt="EMDB" height="35px"/></a> </div> <div class="col-sm-6"> <div class="float-right text-right"> <p style="margin-bottom: 0px;"> Prior Support from<br />National Institutes of Health<br />National Institute of General Medical Sciences</p> </div> </div> </div> <div class="row" style="color:#FFF; background-color: #666; padding-top: 3px; padding-bottom: 8px;"> <div class="col-sm-2">   </div> <div class="col-sm-10"> <div class="small float-right text-right" style="margin-top: 8px;" > © 2007-2025 EMDataResource</div> </div> </div> </div> </footer> </div> </div>  <script> $.get("/js/auto.json", function(data){ $("#homequery").typeahead({ source: data, items: 8, minLength: 1, delay: 60, autoSelect: true, }); },'json'); $('#btnSearch').on('click', function () { var url; var searchInput = $('#homequery').val(); //minimum of 3 characters var regex0 = new RegExp ( "(.){3,}" ); var results0 = regex0.exec( searchInput ); if (results0 !== null) { //test for an EMDB id with or without "EMD-" prefix var regex1 = new RegExp ( "^[eE][mM][dD]-[0-9]{4,}$" ); var regex2 = new RegExp ( "^[0-9]{4,}$" ); //pure number 4+ digits var results1 = regex1.exec( searchInput ); var results2 = regex2.exec( searchInput ); if (results1 !== null) { url = "/EMD-" + searchInput.slice(4); window.open(url); } else if (results2 !== null) { url = "/EMD-" + searchInput; window.open(url); } else { url = "/?emdlist=" + searchInput; window.open(url); } } }); </script> </body> </html>