The EM Data Bank or Electron 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 the
European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. , the resource contained over 2,600 entries with a mean resolution of 15Å.
Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the
wwPDB OneDep interface.
Under the NIH Unified Data Resource for CryoEM, the
Research 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 at
RCSB
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo ...
,
EMBL-EBI
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Well ...
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 at
Scripps 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.
See also
*
Cryo-Electron Microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample sol ...
*
Colocalization Benchmark Source
The Colocalization Benchmark Source (CBS) is a free collection of downloadable images to test and validate the degree of colocalization of markers in any fluorescence microscopy studies. Colocalization is a visual phenomenon when two molecules of i ...
References
*
*
*
*
*{{cite journal , last1=Tagari , first1=M. , first2=J. , last2=Tate , first3=G. J. , last3=Swaminathan , first4=R. , last4=Newman , first5=A. , last5=Naim , first6=W. , last6=Vranken , first7=A. , last7=Kapopoulou , first8=A. , last8=Hussain , first9=J. , last9=Fillon , first10=K. , last10=Henrick , first11=S. , last11=Velankar , display-authors=3 , year=2006 , title=E-MSD: improving data deposition and structure quality , journal=Nucleic Acids Research , volume=34 , issue=Database issue , pages=287–290 , doi=10.1093/nar/gkj163 , pmid=16381867 , pmc=1347525
External links
Software tools for molecular microscopyEM Data BankJapan Search page
(EM Navigator in PDBj)
Biological databases
Electron microscopy
Science and technology in Cambridgeshire
South Cambridgeshire District