PDB-IHM

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>PDB-IHM</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=UA-149785490-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-149785490-1'); </script> <link rel="shortcut icon" href="/images/favicon.jpg"> <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> <link href="/css/bootstrap.carousel.css" type="text/css" rel="stylesheet" media="screen, projection, print"> <style> @charset "UTF-8"; /* CSS Document */ a { color: #333399; font-weight: 450; } /* a:visited { color: #333399; } */ a:hover { color:#5353c6; } .clearfloat { /* this class can be placed on a <br /> or empty div as the final element following the last floated div (within the #container) if the #footer is removed or taken out of the #container */ clear:both; height:0; font-size: 1px; line-height: 0px; } body { background-color: #669966 margin: 0; padding: 0; } /** body { padding-top: 20px; padding-bottom: 20px; } **/ .navbar { margin-bottom: 20px; background-color: #003366; } .navbar-nav > li > a { font-color: white; } .nav.navbar-nav li a { color: white; } .navbar-dark .navbar-nav .nav-item .dropdown-menu { background-color: #003366; } .navbar-dark .navbar-nav .nav-item .dropdown-menu .dropdown-item:hover { background-color: grey; } .navbar-dark .navbar-nav .nav-link { color: rgba(255, 255, 255, 0.90); } .navbar-dark .navbar-nav .nav-link:hover, .navbar-dark .navbar-nav .nav-link:focus { color: rgba(255, 255, 255, 1.00); } .navbar-dark .navbar-nav .nav-link.disabled { color: rgba(255, 255, 255, 0.25); }ii .navbar-dark .navbar-text a:hover, .navbar-dark .navbar-text a:focus { color: #fff; } .nav .home { font-weight: bold; color: #fff; } .home-header { display: show; } </style> </head> <body style="background-color: #669966; "> <script type="text/javascript" src="/js/auto.js"></script> <style> .btn-round{ border-radius: 5px; } </style> <div class="container-fluid"> <div class="card" style="border: none; margin-bottom: 0px; margin-right: 10px; margin-left: 30px; "> <div class="float-left"><b><span id="siteid"></span></b></div>  <div class="card-body" style="padding: 0px 0px;background-color: rgba(102,153,102, 0.5); " > <div class="row"> <div class=" col-sm-9" style="margin-left: 0px;"><a href="/index.html"> <img src="/images/logon.png" class="float-left" alt="PDBIHM.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" /> <p><h1 style="margin-left: 0px; color: #003366;">PDB-IHM</h1><h5 class="float-left" style="color: #003366;">System for Archiving Integrative Structures</h5></p>  </a> </div> <div class="col-sm-3 d-flex align-items-end" style="margin-top: 0px;"><h6 onload="autofunction()" id="auto" class="home-header ml-auto" style="margin-right:27px; margin-top:75px; color:#003366"><b><small></small></b></h6></div> </div> </div> <nav class="navbar navbar-expand-xl 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 mr-4"><a class="nav-link" href="/index.html"><span class="home">Home</span></a></li> <li class="nav-item mr-4"><a class="nav-link" href="/about.html"><span class="about">About</span></a></li> <li class="nav-item mr-4"><a class="nav-link" href="/deposit.html"><span class="deposit">Deposit</span></a></li> <li class="nav-item mr-4"><a class="nav-link" href="/contact.html"><span class="contact">Contact</span></a></li> <li class="nav-item"><a class="nav-link" href="/faq.html"><span class="faq">FAQ</span></a></li>  </ul> <form class="form-inline my-2 my-lg-0"> <div class="input-group"> <input type="button" onclick="location.href='/solrsearch.html?query=*:*';" id="allentries" class=" btn-round mr-sm-2" style="background-color: #669966;color:#FFF;border:none;cursor: pointer;" value="Browse Structures" /> <div class="input-group-btn"> <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="Keyword Search (e.g., NPC AND 3DEM)" aria-label="Search PDB-IHM" style="width:325px;"> </div> </div> <button id="btnSearch" class="btn btn-secondary my-2 my-sm-0" type="submit" style="background-color: #669966; margin-right: 10px;" ><img src="/images/search.svg" alt="search" /></button> </form>   <p class="my-2"><a href="#" style="color:#FFF;" data-toggle="modal" data-target="#exampleModalCenter"><small>Search Tips</small></a></p>  <div class="modal fade" id="exampleModalCenter" tabindex="-1" role="dialog" aria-labelledby="exampleModalCenterTitle" aria-hidden="true"> <div class="modal-dialog modal-dialog-centered" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="exampleModalLongTitle">Search Tips</h5> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body"> <h6 style="color: #669966;"><b>Keyword Search</b></h6> <p>Search can be carried out using keywords such as</p> <ul> <li>macromolecular names (e.g., Exosome, p53)</li> <li>accession codes (e.g., PDBDEV_00000012, PDBDEV_00000014)</li> <li>experimental methods used (e.g., NMR, 3DEM, Crosslinking-MS)</li> <li>author names (e.g., Sali, Bonvin)</li> <li>software used (e.g., IMP, HADDOCK, ROSETTA)</li> </ul> <hr/> <h6 style="color: #669966;"><b>Boolean Search</b></h6> <p>Boolean operators are supported. </p> <ul> <li> AND (e.g., Kim AND Crosslinking-MS) </li> <li> OR (e.g., IMP OR HADDOCK) </li> <li> NOT (e.g., ROSETTA NOT Crosslinking-MS) </li> </ul> <hr/> <h6 style="color: #669966;"><b>Wild Card</b></h6> <p>Wild card symbol can be used to handle truncations. </p> <ul> <li> nup* can be used to search for all keywords that start with the phrase 'nup' (e.g., nup82, nup84, nup133). </li> <li> *trans* can be used to search for all keywords that contain the phrase 'trans' (e.g., methyltransferase, transcription). </li> <li> *some can be used to search for all keywords that end with the phrase 'some' (e.g., BBSome, exosome, nucleosome, proteasome). </li> </ul> <hr/> <h6 style="color: #669966;"><b>Phrase Search</b></h6> <p>Search for exact phrases can be carried out using single quotes (e.g., 'Nucleotide excision repair complex'). </p> <hr/> <h6 style="color: #669966;"><b>Attribute Search</b></h6> <p>Search for specific attributes defined in PDBx/mmCIF and IHM dictionaries can be carried out as follows. </p> <ul> <li>entry.id:*28</li> <li>entry.id:PDBDEV_00000012</li> <li>ihm_cross_link_list.linker_type:CYS</li> </ul> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div>  </div> </nav> <div class="card-body">  <div class="row"> <div class="col-xl-8">  <div class="card-header" style="background-color: #E4E4E4;"> <h2>Welcome to PDB-IHM</h2> <p align="justify" >PDB-IHM is a system for archiving structural models obtained using integrative or hybrid modeling, managed by the wwPDB and funded by the NSF, DOE, and NIH. Structural characterization of many complex macromolecular assemblies is increasingly carried out using integrative modeling, where a combination of complementary experimental and computational techniques is used to determine the structure. The structural models obtained through integrative modeling are collected, processed, and disseminated to the public through PDB-IHM. PDB-IHM was recently unified with the PDB archive, serving integrative structures alongside experimental structures. Integrative structures are now provided PDB accession codes and can be accessed from the <a href="https://files.wwpdb.org/pub/">PDB archive</a> and <a href="http://www.wwpdb.org">wwPDB</a>. </p> </div> <br/> <div class="card"> <div class="card-header" style="background-color: #003366; color: #FFF;"> <div class="float-left"><h3>Released PDB-IHM Structures</h3></div> </div> <div class="card-body">  <div class="container my-4">  <div id="multi-item-example" class="carousel slide carousel-multi-item" data-ride="carousel">  <div class="controls-top"> <a class="btn-floating" href="#multi-item-example" data-slide="prev"><i class="fa fa-chevron-left"></i></a> <a class="btn-floating" href="#multi-item-example" data-slide="next"><i class="fa fa-chevron-right"></i></a> </div>   <ol class="carousel-indicators"> <li data-target="#multi-item-example" data-slide-to="0" class="active"></li> <li data-target="#multi-item-example" data-slide-to="1"></li> <li data-target="#multi-item-example" data-slide-to="2"></li> </ol>   <div class="carousel-inner" role="listbox">  <div class="carousel-item active"> <div class="row"> <div class="col-md-4 d-flex align-items-stretch"> <div class="card mb-2"> <img class="card-img-top" src="/images/8zzc_resize_1.png" alt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; "> <p class="card-title text-center mysize" style="font-size:0.9em;"><a href="entry.html?8ZZC"><b>8ZZC</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>Nuclear pore complex</b></p> <p class="card-text text-center" style="color:#669966 ;"><small>Release Date: 2018-03-09 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1038/nature26003">10.1038/nature26003</a></i></small></b> </div> </div> </div> <div class="col-md-4 clearfix d-flex align-items-stretch"> <div class="card mb-2"> <img class="card-img-top" src="/images/8zze_resize_1.png" alt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; overflow:hidden;"> <p class="card-title text-center" style="font-size:0.9em;"><a href="entry.html?8ZZE"><b>8ZZE</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>16S rRNA and methyltransferase A complex</b></a></p> <p class="card-text text-center" style="color:#669966 ;"><small>Release Date: 2018-02-09 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1016/j.str.2015.03.014">10.1016/j.str.2015.03.014</a></i></small></b> </div> </div> </div> <div class="col-md-4 clearfix d-flex align-items-stretch"> <div class="card mb-2 "> <img class="card-img-top" src="/images/8zzi_resize_1.png" lt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; overflow:hidden;"> <p class="card-title text-center" style="font-size:0.9em;"><a href="entry.html?8ZZI"><b>8ZZI</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>BBSome complex</b></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2019-09-05 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1016/j.str.2019.06.006">10.1016/j.str.2019.06.006</a></i></small></b> </div> </div> </div> </div> </div>   <div class="carousel-item"> <div class="row"> <div class="col-md-4 d-flex align-items-stretch"> <div class="card mb-2"> <img class="card-img-top" src="/images/8zzs_resize_1.png" alt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; "> <p class="card-title text-center mysize" style="font-size:0.9em;"><a href="entry.html?8ZZS"><b>8ZZS</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>RNF168-RING domain and nucleosome complex</b></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2019-04-29 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1038/s41467-019-09756-z">10.1038/s41467-019-09756-z</a></i></small></b> </div> </div> </div> <div class="col-md-4 clearfix d-flex align-items-stretch"> <div class="card mb-2"> <img class="card-img-top" src="/images/8zzu_resize_1.png" alt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; overflow:hidden;"> <p class="card-title text-center" style="font-size:0.9em;"><a href="entry.html?8ZZU"><b>8ZZU</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>Human Fibrin Clots</b></a></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2020-01-10 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1073/pnas.1911785117">10.1073/pnas.1911785117</a></i></small></b> </div> </div> </div> <div class="col-md-4 clearfix d-flex align-items-stretch"> <div class="card mb-2 "> <img class="card-img-top" src="/images/8zzw_resize_1.png" lt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; overflow:hidden;"> <p class="card-title text-center" style="font-size:0.9em;"><a href="entry.html?8ZZW"><b>8ZZW</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>HCN Channel Voltage Sensor</b></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2019-07-06</small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1038/s41594-019-0259-1">10.1038/s41594-019-0259-1</a></i></small></b> </div> </div> </div> </div> </div>   <div class="carousel-item"> <div class="row"> <div class="col-md-4 d-flex align-items-stretch"> <div class="card mb-2"> <img class="card-img-top" src="/images/9a00_resize_1.png" alt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; "> <p class="card-title text-center mysize" style="font-size:0.9em;"><a href="entry.html?9A00"><b>9A00</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>Myeloid-derived growth factor with KDEL receptor</b></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2019-12-18 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1038/s41467-019-13577-5">10.1038/s41467-019-13577-5</a></i></small></b> </div> </div> </div> <div class="col-md-4 clearfix d-flex align-items-stretch"> <div class="card mb-2"> <img class="card-img-top" src="/images/9a01_resize_1.png" alt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; overflow:hidden;"> <p class="card-title text-center" style="font-size:0.9em;"><a href="entry.html?9A01"><b>9A01</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>Human COP9 Signalosome</b></a></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2020-01-30 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1073/pnas.1915542117">10.1073/pnas.1915542117</a></i></small></b> </div> </div> </div> <div class="col-md-4 clearfix d-flex align-items-stretch"> <div class="card mb-2 "> <img class="card-img-top" src="/images/9a03_resize_1.png" lt="Card image cap"> <div class="card-body" style="background-color: #F0F0F0; overflow:hidden;"> <p class="card-title text-center" style="font-size:0.9em;"><a href="entry.html?9A03"><b>9A03</b></a></p> <p class="card-text text-center" style="color:#404040; font-size:0.90em;"><b>Nucleotide excision repair complex</b></p> <p class="card-text text-center" style="color:#669966;"><small>Release Date: 2020-02-07 </small></b><br/> <p class="card-text text-center" style="color:#000;"><small><i>Publication doi: <a href="https://dx.doi.org/10.1093/nar/gkz1231">10.1093/nar/gkz1231</a></i></small></b> </div> </div> </div> </div> </div>  </div>  </div>  </div> </div> </div> </div> <div class="col-xl-4"> <div class="card">  <div class="card-header" style="background-color: #E4E4E4;">  <div class="float-left"><h3>News</h3></div> <div class="float-right" style="margin-top:10px;"><h3><a style="font-size:large;" href="allnews.html"> All News</a></h3></div> </div> <div class="card-body">  <h5><a title="PDB-Dev rebranded as PDB-IHM" href="/allnews.html#collapseTwenty">PDB-Dev rebranded as PDB-IHM</a></h5> <p align="justify" style="font-size: 1.0em;"> In August 2024, PDB-Dev was unified with the PDB to deliver integrative structures alongside archived experimental structures in the PDB archive. Following the unification, PDB-Dev has now been rebranded as PDB-IHM. <a title="Read the rest of this posting." href="/allnews.html#collapseTwenty"><strong>Read more...</strong></a></p> </p> <br/> <h5><a title="wwPDB DOIs and DOI Landing Pages for Integrative Structures" href="/allnews.html#collapseNineteen">wwPDB DOIs and DOI Landing Pages for Integrative Structures</a></h5> <p align="justify" style="font-size: 1.0em;"> Integrative structures are now available at wwPDB Digitial Object Identifier (DOI) landing pages, along with >225,000 experimental structures in the PDB archive. DOI landing pages are available for both released and on-hold entries in PDB-IHM. <a title="Read the rest of this posting." href="/allnews.html#collapseNineteen"><strong>Read more...</strong></a></p> </p> <br/> <h5><a title="Integrative Structures in the PDB Archive" href="/allnews.html#collapseEighteen">Integrative Structures in the PDB Archive</a></h5> <p align="justify" style="font-size: 1.0em;">Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. Users can access and download IHM structures and associated data from the <a href='https://files.wwpdb.org/pub/pdb_ihm/'>PDB archive</a>. Currently, holding files in JSON format, validation reports (summary and full reports) in PDF format, and model files in PDBx/mmCIF format are provided. <a title="Read the rest of this posting." href="/allnews.html#collapseEighteen"><strong>Read more...</strong></a></p> </p> <br/> <h5><a title="PDB Accession Codes for Integrative Structures" href="/allnews.html#collapseSeventeen">PDB Accession Codes for Integrative Structures</a></h5> <p align="justify" style="font-size: 1.0em;">Integrative structures deposited to PDB-IHM will now be issued 4-character PDB accession codes (e.g., 8ZZ1). Going forward all new depositions will only be issued PDB accession codes and PDB-IHM accession codes (e.g., PDBDEV_00000001) will not be issued. Existing entries have been remediated to include new PDB accession codes and re-released. The PDB-IHM website will support search and access of integrative structures using both PDB and PDB-IHM accession codes. <a title="Read the rest of this posting." href="/allnews.html#collapseSeventeen"><strong>Read more...</strong></a></p> </p> <br/> <h5><a title="IHMCIF Publication" href="/allnews.html#collapseSixteen">IHMCIF Publication</a></h5> <p align="justify" style="font-size: 1.0em;">IHMCIF, the data standard underpinning the PDB-IHM system, has been published in the 2024 Special Issue on Computation Resources in the Journal of Molecular Biology: Vallat B et al., IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods, J Mol Biol. 2024; 168546. doi: <a href="https://doi.org/10.1016/j.jmb.2024.168546">10.1016/j.jmb.2024.168546</a>. <a title="Read the rest of this posting." href="/allnews.html#collapseSixteen"><strong>Read more...</strong></a></p> </p> <br/> </div>  </div>  </div>  </div>  </div>  <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="/color:#FFF; background-color: rgba(102,153,102, 0.5); ; padding-top: 10px; padding-bottom: 2px;"> <div class="col-sm-6" style="padding-top: 10px; padding-bottom: 10px;"> <a href="http://www.wwpdb.org/" target="_blank"> <img src="/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"/></a> </div>  <div class="col-sm-6"> <div class="float-right text-right"> <p style="margin-bottom: 0px; margin-right: 0px;color: #000"> Supported by<br />NSF, DOE, NIH</p> </div> </div> </div> <div class="row" style="color:#FFF; background-color: #669966; padding-top: 3px; padding-bottom: 8px;">  </div> </div> </div> </footer> <script> $.get(function(data){ $("#homequery").typeahead({ source: data, items: 8, minLength: 1, delay: 60, autoSelect: true, }); },'json'); $('#btnSearch').on('click', function () { var url; var searchInput = $('#homequery').val(); //if (searchInput) { url = "solrsearch.html?query=" + searchInput; window.open(url); } //minimum of 3 characters var regex0 = new RegExp ( "(.){3,}" ); var results0 = regex0.exec( searchInput ); if (results0 !== null) { //test for an PDB-IHM id with or without "PDBDEV" prefix var regex1 = new RegExp ( "^[pP][dD][bB][dD][eE][vV]_[0-9]{8,}$" ); var regex2 = new RegExp ( "^[0-9]{8,}$" ); //pure number 8+ digits var results1 = regex1.exec( searchInput ); var results2 = regex2.exec( searchInput ); if (results1 !== null) { url = "entry.html?PDBDEV_" + searchInput.slice(7); window.open(url); } else if (results2 !== null) { url = "entry.html?PDBDEV_" + searchInput; window.open(url); } else { url = "solrsearch.html?query=" + searchInput; window.open(url); } } }); </script> </div> <script type="text/javascript"> //randomize first active slide var currentSlide; var rand; $(document).ready(function() { currentSlide = Math.floor((Math.random() * $('.carousel-item').length)); rand = currentSlide; $('#PDBCarousel').carousel(currentSlide); // $('#PDBCarousel').fadeIn(1000); }); </script> <script type="text/javascript" src="/js/ihmsearch.js"></script> <script> $(document).ready(on_ready); </script> </body> </html>

CINXE.COM

PDB-IHM