TheEM Data Bank orElectron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of theEuropean Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located.[2] As of 2015[update], the resource contained over 2,600 entries with a mean resolution of 15Å.[3]
Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into thewwPDB OneDep interface.[4]
Under the NIH Unified Data Resource for CryoEM, theResearch Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB.
EM Data Bank also provides the EMsearch search tool and data can also be queried atRCSB,EMBL-EBI and PDBj.
EMDB is an archive for three-dimensional density maps of all types of biological assemblies, including ribosomes, chaperones, polymerases, multifunctional enzymes and viruses. Viper EMDB atScripps is a separate database for three-dimensional EM maps of viruses.
To compare and assess methods for the new generation of higher resolution (better than 5Å) structures, the EMDB has hosted the first CryoEM Map Challenge and CryoEM Model Challenge, reported in a special issue of the Journal of Structural Biology.[5]
Tagari, Mohamed; Newman, Richard; Chagoyen, Monica; Carazo, Jose-Maria; Henrick, Kim (2002). "New electron microscopy database and deposition system".Trends in Biochemical Sciences.27 (11): 589.doi:10.1016/s0968-0004(02)02176-x.PMID12417136.
Henrick, K; Newman, R; Tagari, M; Chagoyenb, M (2003). "EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information".Journal of Structural Biology.144 (1–2):228–237.doi:10.1016/j.jsb.2003.09.009.PMID14643225.
Heymann, J. Bernard; Chagoyen, Mónica; Belnap, David M. (2005). "Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology".Journal of Structural Biology.151 (2):196–207.doi:10.1016/j.jsb.2005.06.001.PMID16043364.
