Research Collaboratory For Structural Bioinformatics - Rcsb
RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICSRutgers, The State University of New JerseyUniversity of California, San Diego1
About the CoverSince January 2000, the RCSB PDB's Molecule of the Month has been introducing readers to the structure and function of the many nucleic acids,proteins, and complex assemblies found in the PDB.The cover of this report represents a new way of navigating through thearchive of past Molecule of the Month columns. Each article has been sortedinto a category or categories based on biological context.Table of ContentsEach structure shown represents a major, top-level functional category:About the Cover.2Message from the Director .3About the RCSB PDB.4Snapshot: July 1, 2010 .4The PDB Archive of Biomolecular Structures.4What Does the PDB Enable?.5The RCSB Protein Data Bank .5The Worldwide Protein Data Bank.5The RCSB PDB Organization .6Funding .6Data Input.7Before Structures Enter the Archive:Data Deposition, Validation, and Annotation.7Deposition Statistics.7Software for Deposition and Validation.8Validation Reports .8Deposition in the Future: The wwPDBCommon Deposition & Annotation Tool.8Data Access, Query, and Reporting.9Data Distribution and Access.9Website Overview .9Exploring Structures .9Data Query and Reporting .10New Features .11MyPDB.11Time-stamped Archival Copies .11User Outreach.12Community Interactions.12Online Help.12Publications .12Educational Initiatives .13Online Features .13Educational Programs and Activities.13Related Resources .14Structural Genomics and the PSIStructural Biology Knowledgebase .14BioSync .14EMDataBank.org .14References .15Molecule of the Month Illustration References.16PROTEIN SYNTHESIS includes the major molecules ofprotein synthesis, from DNA to RNA to ribosomes tofolded proteins.Example: ribosomedoi: 10.2210/rcsb pdb/mom 2000 10BIOTECHNOLOGY AND NANOTECHNOLOGYexplores the ways scientists look to nature forinspiration, and harness biological machinery for usein science and technology.Example: designed DNA crystaldoi: 10.2210/rcsb pdb/mom 2009 11HEALTH AND DISEASE covers subjects such as drugaction, viruses, and the molecular basis of disease.Example: rhinovirusdoi: 10.2210/rcsb pdb/mom 2001 8INFRASTRUCTURE AND COMMUNICATION includestopics such as structural proteins and cell signaling.Example: collagendoi: 10.2210/rcsb pdb/mom 2000 4BIOLOGICAL ENERGY presents the processes forcapturing and converting energy in cells.Example: photosystem Idoi: 10.2210/rcsb pdb/mom 2001 10The ENZYMES category organizes the many catalystsfor all of the chemical transformations needed for life.Example: phosphofructokinasedoi: 10.2210/rcsb pdb/mom 2004 2From these major topics, readers can browse descriptive subcategories thatlead to the individual Molecule of the Month features. The Protein Synthesiscategory, for example, contains subcategories about the Structure of NucleicAcids, DNA Maintenance, Replication, Transcription, Translation, and ProteinFolding/Modification/Degradation. Each subcategory then reveals the relevantMolecule of the Month features. All articles can still be searched by date andfeature title, but the category view lets users approach the Molecule of the Montharchive with a biological interest, rather than a specific molecule, in mind.We hope that this new interface will promote new ways of exploring thesearticles and the PDB archive.Molecule of the Month articles can be referenced and accessed using their Digital Object Identifiers(DOI). The DOI can be used as part of a URL (http://10.2210/rcsb pdb/mom 2000 10), orentered in a DOI resolver (such as http://www.crossref.org/) to automatically link to thefeature at the RCSB PDB website.
Message from the DirectorThe Protein Data Bank (PDB) is the central archive of the 3Dstructures of biological molecules. Originally developed as arepository for the structural biology community, it has grown inthe past 39 years to serve a wide range of communities. Scientistsfrom around the world depend upon PDB data for their researchand discoveries, while students and teachers access the PDB tostudy biological processes and medicine at the molecular level.The PDB is by nature community-based. The archive itself iscomprised of experimental data contributed by structural biologists.The free and open sharing and exchange of this data then drivesscience and education worldwide.In partnership with the Worldwide Protein Data Bank, the RCSBPDB curates, annotates, and distributes PDB data. This collaborationensures that PDB data are provided in an accurate and timelymanner, and in a single, uniform, and global PDB archive.The RCSB PDB website provides access to the PDB, along withrelated tools and resources to examine these structures in the contextof function, biological processes, evolution, pathways and diseasestates. Conversations and feedback from RCSB PDB users guidethe development of comprehensive, integrated, and unique viewsof the data that enable scientific innovation and education.This report highlights the key components of the RCSB PDB–"data in", "data out", and outreach and education–along withthe major highlights of the report period of July 1, 2009 - June30, 2010. These activities promote access to and understandingof the PDB archive, with the goal of serving both the scientificand educational communities.Helen M. BermanDirector, RCSB PDBBoard of Governors Professor of Chemistryand Chemical BiologyRutgers, The State University of New JerseyPDB ID: 2x5uLight-induced structural changes in a photosynthetic reaction center caught by Laue diffraction.A.B. Wohri, G. Katona, L.C. Johansson, E. Fritz, E. Malmerberg, M. Andersson,J. Vincent, M. Eklund, M. Cammarata, M. Wulff, J. Davidsson, G. Groenhof, R. Neutze (2010) Science 328: 630-6333
About the RCSB PDBSnapshot: July 1, 2010Number of Entries66212 released atomic coordinateentriesThe PDB Archive of Biomolecular StructuresEntries by Molecule Type61280 proteins, peptides, and viruses2746 protein/nucleic acid complexes2148 nucleic acids38 otherEntries by Experimental Technique57298 X-ray8449 NMR295 electron microscopy24 hybrid methods146 otherRelated Experimental Data46690 structure factor files5742 NMR restraint filesAs the single repository of information about the 3D structures of proteins, nucleic acids,and complex assemblies, the Protein Data Bank (PDB) archive1-3 is a vital resource forworldwide research and study in the biomedical and agricultural sciences.The archive contains biomolecules determined from experiments in X-ray crystallography,nuclear magnetic resonance (NMR), and electron microscopy. From around the world,scientists determine the atomic arrangements of these molecules, and submit data abouttheir experiments to the PDB. This information is processed, validated, annotated, andmade publicly available, at no cost, to the global community.Countless individual users and external resources require PDB data for their study andresearch. By comparing the many structures available in the PDB, structural biologists havemade basic discoveries in molecular evolution, enzyme action, molecular recognition,protein folding and assembly, and countless other central biological concepts. The structuresin the PDB have been widely used for the development of new pharmaceutical agents; forinstance, drugs developed from structures in the PDB have changed HIV infection from auniformly deadly disease into a treatable condition. The broader community of biologistsuses the structures in the PDB, augmented by sequence information and other data, to lendstructural insight to their work, for instance, exploring the structural consequences ofmutations. Finally, the PDB is widely used in the education and outreach community tocreate dynamic imagery that brings the results of basic and applied biological research tothe general public.As of July 2010, the PDB archive containedPublic archive (109 GB) More than 66,000 entries More than 500,000 files Data dictionaries and documentation Derived data filesFor each PDB entry Atomic coordinates Sequence information Description of structure Experimental dataInternal archive Depositor correspondence Depositor contact information Paper records Documentation Historical recordsThe structures archived in the PDB are vital to the study of science and medicine worldwide.The examples shown below have been highlighted in past Molecule of the Month features.4Cholera ToxinAntibodiesDNAHIV-1 Proteasedoi: 10.2210/rcsb pdb/mom 2005 9doi: 10.2210/rcsb pdb/mom 2001 910.2210/rcsb pdb/mom 2001 11doi: 10.2210/rcsb pdb/mom 2000 6
What Does the PDB Enable?Through the safe storage and free access to the scientific data in thePDB archive, scientists and students can Decipher the functions of molecules with known sequence andstructure, but unknown biochemical function Study evolution over long-time scales where the sequence signalindicating a relationship is too weak to measure Better understand regulation, signaling and other pathways Study protein motion and allostery Explore the underlying mechanisms of organ systems in the humanbody, from circulatory to lymphatic to urinary systems Design drugs that will respond to emerging infectious diseases Understand biological principles in detail Predict and develop models for proteins with unknown 3D structurePDB ID: 2ku1Dynamic regulation of archaeal proteasome gate opening asstudied by TROSY NMR. T. L. Religa, R. Sprangers, L. E. Kay (2010)Science 328: 98-102The RCSB Protein Data BankThe Worldwide Protein Data BankThe RCSB Protein Data Bank, administered by the Research Collaboratory for Structural Bioinformatics (RCSB),2 provides a global resource for the advancement of research and education in biology andmedicine by curating, integrating, and disseminating biologicalmacromolecular structural information in the context of function,biological processes, evolution, pathways, and disease states.The wwPDB organization(www.wwpdb.org)1 is a uniquescientific collaboration thatprovides the authoritativeresource for experimentallydetermined 3D structures of biological macromolecules. It wasformed to ensure that the PDB archive, now and in the future, is freelyand publicly available to the global community. wwPDB members(RCSB PDB, Protein Data Bank in Europe (PDBe),4 Protein DataBank Japan (PDBj),5 and the BioMagResBank (BMRB)6) hostdeposition, processing, and distribution centers for PDB data andcollaborate on a variety of projects and outreach efforts.As a member of the Worldwide PDB (wwPDB), the RCSB PDB supports the deposition, processing, and annotation of experimentalstructure data. As the archive keeper for the wwPDB, the RCSB PDBmaintains the PDB central repository.The RCSB PDB’s website offers a searchable database, tools, and related services for users to easily search, analyze, and visualize the datain the PDB archive. These efforts are enhanced by targeted educationand outreach activities.ThrombinEstrogen Receptordoi: 10.2210/rcsb pdb/mom 2002 1doi: 10.2210/rcsb pdb/mom 2003 9A major focus of the wwPDB is maintaining consistency and accuracyacross the archive. As the PDB grows, new structures and new technologies can challenge how all structures are represented. To helpface these situations, the wwPDB regularly reviews data processingprocedures, coordinates "remediation" efforts to improve data representation in the archive, and implements policies and standards toaccommodate new developments in structural biology. Policies aredeveloped in concert with the wwPDB Advisory Committee and withValidation Task Forces comprised of experts in the experimentalmethod communities. These Task Forces have been convened to collect recommendations and develop consensus on additional validation that should be performed, and to identify software applicationsto perform validation tasks.5
About the RCSB PDBFundingThe RCSB PDB is supported byfunds from:The RCSB PDB OrganizationThe RCSB PDB is jointly managed at Rutgers, The State University ofNew Jersey and the San Diego Supercomputer Center and the SkaggsSchool of Pharmacy and Pharmaceutical Sciences at the University ofCalifornia, San Diego.Helen M. Berman, Director of the RCSB PDB, is a Board of Governorsprofessor of chemistry and chemical biology at Rutgers. ProfessorBerman was part of the team that first envisioned the PDB archive. Dr.Martha Quesada, Deputy Director (Rutgers), and Professor Philip E.Bourne, Associate Director (UCSD), join her in RCSB PDB management.The RCSB PDB Team is comprised of experts in diverse fields ofcomputer science, biology, chemistry, and education. In addition toworking with PDB data, RCSB PDB members co-author scientificpapers, exhibit at meetings, present posters and papers, and attendand organize workshops. Staff members also serve as tutors, teachers,and mentors to students of all ages.The RCSB PDB receives input from an advisory board of experts inX-ray crystallography, NMR, 3D EM, bioinformatics, and education(the RCSB PDB Advisory Committee).The RCSB PDB team and collaborators6 National ScienceFoundation (NSF) National Institute of GeneralMedical Sciences (NIGMS) Office of Science,Department of Energy (DOE) National Library of Medicine(NLM) National Cancer Institute(NCI) National Institute ofNeurological Disorders andStroke (NINDS) National Institute ofDiabetes & Digestive &Kidney Diseases (NIDDK)NIGMS
Data InputDeposition StatisticsJuly 1, 2009– June 30, 2010Before Structures Enter the Archive:Data Deposition, Validation, and AnnotationThe data in the PDB is contributed from scientists located around theworld, and then validated and curated by the wwPDB before beingmade publicly available in the archive.7When a structure is deposited online, it is immediately assigned itsown unique PDB ID. Approximately 25 new entries are deposited tothe PDB each day. Using locally-developed tools, the RCSB PDB carefully curates and annotates entries using an integrated system thatuses a standard data dictionary for macromolecular structure8 and forthe small chemical components found in PDB entries. The goal is thatPDB entry accurately represents the structure and experiment.Annotation-curators check each deposition for errors or omissions,and compare the reported sequence, source, and other informationwith external databases.9-10 The entry is assigned a title, names andsynonyms for the protein or other polymer, scientific name of macromolecule's source, and biological assembly information. After reviewing the structure visually, the completed entry is sent to the depositor,along with a summary validation report. Annotators then work withthe depositor to address any issues and finalize the entry for publicrelease. On average, this process takes two weeks.Depending upon the hold status selected by the depositor, datarelease occurs when a depositor gives approval to the finalized entry(status: REL), the hold date has expired (HOLD), or the journal articledescribing the structure has been published (HPUB). Structurescan be on HOLD or HPUB for no longer than one year past the dateof deposition.7848 structures were deposited to the PDB archive andprepared for release by the wwPDB during the period ofthis report. 6860 of these entries were deposited to theRCSB PDB.Sequences for 55% of these depositions were made publiclyavailable before the coordinate files. This helps to preventduplication of structure determination effort and promotesblind testing of structure prediction and modeling techniques.wwPDB Processing SiteRCSB PDB: 62%PDBj: 25%PDBe: 13%Author-defined Release StatusHPUB: 75%REL: 21%HOLD: 4%Experimental SourceX-ray Crystallography: 92%NMR: 7%Growth in Data Depositions (2000-2009)Electron Microsopy: 1%Hybrid: 1%Other: 1%Depositor LocationNorth America: 46%Europe: 28%Asia: 16%South America: 1%Australia/NewZealand: 2%Africa: 1%Industry: 7%PDB ID: 3k3fCrystal structure of a bacterial homologue of the kidney ureatransporter. E.J. Levin, M. Quick, M. Zhou (2009)Nature 462: 757-7617
Data InputwwPDB Validation ReportsReviewSoftware for Deposition and ValidationThe RCSB PDB develops tools that facilitate data validation andsubmission for depositors, even as structures are in the process ofbeing determined. Software downloads, web servers, and documentation are available at deposit.pdb.org. pdb extract15 automatically puts key details from the output filesproduced by many NMR and X-ray crystallographic applications in adeposition-ready format. SF-Tool validates model coordinates against structure factor data,translates structure factors into different formats, and checks fortwinned data. The Validation Server checks the format of the coordinate file andvalidates the overall structure before deposition. Researchers areencouraged to use this program to review the quality of any releasedstructure before using it in their own study. The RCSB PDB and PDBj use ADIT2 for data deposition andannotation. Depositors upload their data files and use the ADITeditor to add information and check the completeness of an entry. Anew and improved version of ADIT was released during this reportperiod. With this version, depositors are required to run validationchecks before the entry is deposited.ADIT-NMR, a similar program hosted at BMRB and PDBj, is a singletool for NMR structural and experimental data deposition. Coordinates and constraint data are processed and released by the RCSB PDBand PDBj, while other NMR spectral data are processed and archivedby BMRB. Similarly, EMDep integrates map deposition to EMDB andmodel coordinate deposition to PDB.Annotators use a special version of ADIT to prepare entries for release. Ligand Expo provides tools for accessing, visualizing, and viewingreports about the information in the wwPDB's Chemical ComponentDictionary. It can also be used to identify structure entries containingparticular small molecules; browse tables of components that containoutput fromvalidationprogramsRespondto any issuesShareValidation is the process of checkingsubmitted values against communityaccepted standards. It helps to ensurethat the data deposited and releasedin the PDB are accurate. The results ofvalidation checking also provide away of assessing the “quality” of astructure.As part of the structure annotationprocess, wwPDB members providedepositors with detailed validation reports that include the results of geometric and experimental datachecking.11-14 These reports, availableas PDFs, can be easily reviewed andshared by depositors.with journalsand coauthorsAs these validation reports providean assessment of structure qualitywhile keeping the coordinate dataconfidential, we are encouragingjournal editors and referees to request them from depositors as part of the manuscript submission and review process. PDB validation reports arealready required by the International Union of Crystallography (IUCr) journals as part of their submission process. Thereports will continue to be developed and improved as we receive recommendations from our Validation Task Forces andas we further develop our data deposition and processing procedures.modified amino acids, nucleotides, popular drugs (trade and genericnames) and common ring systems; review related information inchemical dictionaries and resource files; and download the 3D structureof small molecule components. A sketch tool is also provided forbuilding new chemical definitions from reported PDB chemicalcomponents. This tool is used by annotators and by depositorspreparing submissions.Deposition in the Future: The wwPDB Common Deposition & Annotation ToolWhile the wwPDB partners follow established procedures and formats for data processing, different tools areused for the annotation of data, depending upon what data were deposited and where. The wwPDB partnershave started a project to produce a set of common deposition and annotation processes and tools thatwill enable the wwPDB to deliver a resource of increasingly high quality and dependability over thenext 10 years. Specifically, the new processes and supporting systems will address the anticipatedincrease in complexity and experimental variety of submissions over a 10-year life span along withthe increase in deposition throughput. The processes and tools will maximize the efficiency andeffectiveness of data handling and support for the scientific community.The tool is being developed module by module. Work during the period of this report has focusedon the sequence and the ligand processing modules, and on the overall workflow manager. Thesemodules are integrated with external resources and visualization tools.This single, common tool is being developed by the wwPDB following standard project managementprocedures. Made up of experts from all partner sites, the project team meets regularly and works inconversation with the wwPDB Directors and the depositing community.8
Data Access, Query, and ReportingData Distribution and AccessWebsite OverviewRCSB PDB services and data are freely available online.Recently, RCSB PDB web pages were reorganized in response to user feedback. Navigating the website and search results is easier and more intuitive.As the archive keeper for the wwPDB, the RCSB PDB maintains the PDBarchive at ftp://ftp.wwpdb.org. It has sole write access to the FTP archive,and controls updates and distribution to our global partners. Updates ofthe PDB archive and the wwPDB websites are coordinated to occur at thetarget time of Wednesday 00:00 UTC (Tuesday 5:00 p.m. Pacific).During this report period, 7835 PDB entries (in PDB, mmCIF, andPDBML/XML file formats), 7422 structure factor files, and 551constraint data files were added to the archive.The RCSB PDB website at www.pdb.org is a portal to these data files.The website also provides access to a relational database that integrates these data with more than 30 external sources of related data(e.g., sequence annotations, structure annotations, taxonomy, functional descriptors), tools for visualization, and related editorial andeducational content. The website is accessed by about 180,000unique visitors per month from more than 150 different countries.Around 1 terabyte of data is transferred each month this way. At thesame time, about 11,000 unique visitors download more than 14million files from the FTP site, for a total of about 2 terabytes of data.Data are also accessed through Web Services that allow remote software to search the RCSB PDB database and retrieve data for any givenstructure. These services, including the new RESTful Web Services, helpdevelopers create tools that interact efficiently with PDB data.Much of the website, including the home page, uses customizableweb widgets. Boxes with a dark blue bar on top are widgets that canbe moved on the page by dragging the arrow buttons, hidden by selecting "Hide," or included in a customized view. The left-hand menunow groups frequently-used web pages into sections–Deposition,Home, Search, Tools, My PDB, Help, and Education–that can bemoved up and down to order by user interest. New widgets on thehome page display and link to all entries released in the most recentupdate in the Latest Structures widget, while the New Features widgettiles through the enhancements recently added to the website, withlinks to detailed information.Exploring Individual StructuresFor every entry in the PDB, an RCSB PDB Structure Summary pageprovides an overview of the structure; derived data from CATH, SCOP,Pfam, and Gene Ontology (GO);16-19 tools to examine the sequence,sequence domains, and sequence similarity; detailed information relatingto the entry’s citation, biology and chemistry, experiment, and geometry;and links to related resources. Several molecular viewers, includingJmol20 and the RCSB PDB’s Protein Workshop and Ligand Explorer,21help users view the molecule interactively. A Literature view optionprovides the abstract and related details about the reference describing the structure, and includes information about other articles referencing the entry.22Unique Visitors and Visits to www.pdb.org (July 1, 2009 - June 30, 2010)Unique VisitorsGrowth in Website Access (2007-2010)Visits9
Data Access, Query, and ReportingData Query and ReportingThe website provides access to a relational database23-24 that integratesPDB data with related information from external sources (such asjournal abstracts, functional descriptors, sequence annotations, structureannotations, and taxonomy). Users can search for structures usingsimple searches (PDB ID, keyword, sequence, or author) or by buildingmore complex queries with the tool Advanced Search.PDB structures can be browsed using tree-like hierarchies based on GOterms, Enzyme Classification,25 Medical Subject Headings, SourceOrganism, Genome Location,10 SCOP, and CATH classifications.Data downloads fromftp.wwpdb.orgAll search result sets can be explored or further refined. Individualstructures can be examined at any point. Search results can bepresented as a list of structures matching the query; a PubMed-likelist of the primary citations for the structures; a list of ligands knownto interact with the structures; a list of any RCSB PDB web pages thatcontain a particular keyword, including Molecule of the Month features;and a list of corresponding GO, SCOP, or CATH hits.RCSB PDB website features are supported by help pages, tutorials,and an active help desk. Additional enhancements and new resourcesare continually in development.Data downloads per month from www.pdb.org in GB(July 1, 2009 - June 30, 2010)Yearly growth in GB of webdata downloads (2007-2010)During this report period,ftp://ftp.wwpdb.org hosted 174,571,033 total downloads(14138 GB) An average of 129,165 uniqueusers each monthThe number of downloads in 2009reflects the release of a standardizedversion of the entire archive.Website User Location (July 1 - June 30, 2010)North America:33%Europe: 32%Asia: 27%South America: 4%Australia/New Zealand: 2%Africa: 2%Web traffic by country. Image from Google Analytics.10Web traffic by continent.
The MyPDB service automatically emails alerts when thePDB releases entries that match user-stored queries.New FeaturesWith MyPDB, users canThe Comparison Tool calculates pairwise sequence (blast2seq,Needleman-Wunsch, and Smith-Waterman)26-28 and structure alignments (FATCAT, CE, Mammoth, TM-Align, TopMatch).29-34Comparisons can be made for anyprotein in the archive and for customized or local files not in thePDB. Special features include support for both rigid-body and flexible alignments (via jFATCAT) anddetection of circular permutations(via jCE).35 jFATCAT and jCE alignments are performed on RCSBPDB servers, while Mammoth,TMAlign, and TopMatch comparisons are calculated by throughlinks to the corresponding sites.Structure alignment of twonucleotide-binding proteins.36-37The Comparison Tool's jCE optioncan detect the circular permutations that are difficult for manyalignment algorithms to detect. combine and save keyword, sequence, ligand and othersearches refine and/or run stored searches at any time receive email alerts weekly or monthlyTo subscribe, select the MyPDB registration option from theleft-hand menu at www.pdb.org.Display of Large Assemblies: Providing a simple interactive view ofextremely complex structures has been challenging. The RCSB PDB'sJmol view now supports all entries, including extremely large ribosome complexes split across multiple entries, and vault structures thatcontain a very large number of atoms and chains. Composite viewsof split entries can also be displayed for asymmetric units and the biological assemblies.The Comparison Tool is availablefrom the RCSB PDB as a web page,web widget, and stand-alone JavaWeb Start application. It is alsointegrated with the Sequence Clusters offered from each entry'sSequence Similarity Tab.Ligand searching and reporting for ligands using the AdvancedSearch, the Chemical Structure Search, or the top-bar pulldown hasbeen greatly improved. The Chemical Name search from the top-bar pulldown on everypage returns matches to names of small molecules in the wwPDBChemical Component Dictionary and any synonyms. Searches byChemical Name or ID will return structures with matching chemicalcomponents that are free ligands or are part of a protein or nucleicacid chain. In Advanced Search, searches can be specified to look for free and/orpolymeric chemical components. A "sounds like" option searches formisspelled or incomplete names. Advanced Searches using SMILESstrings us
oratory for Structural Bioinformatics (RCSB),2provides a global re-source for the advancement of research and education in biology and medicine by curating, integrating, and disseminating biological macromolecular structural information in the context of function, biological processes, evolution, pathways, and disease states.
Structural bioinformatics adds scale and precision Structural Bioinformatics Structure Prediction Integrative Methods Molecular Simulation Structure Alignment Functional Site Comparison Docking . Lehigh University BioS 10: BioSciences in the 21st Century Brian Y. Chen Many computational fields support Structural Bioinformatics Structural
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