EM Data Bank

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EMDataBank.org
Database.png
Content
Description Unified Data Resource for CryoEM.
Contact
Research center European Bioinformatics Institute (UK site) AND Rutgers University (USA site)
Laboratory PDBe & RCSB PDB
Primary citation Lawson & al. (2011)[1]
Release date 2002
Access
Website http://emdatabank.org

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. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.[2]

Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface[3]

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, 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 at Scripps is a separate database for three-dimensional EM maps of viruses.

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References[edit]

  1. ^ Lawson, Catherine L; Baker, Matthew L; Best, Christoph; et al. (January 2011). "EMDataBank.org: unified data resource for CryoEM". Nucleic Acids Research. 39 (suppl 1): D456–464. doi:10.1093/nar/gkq880. PMC 3013769Freely accessible. PMID 20935055. 
  2. ^ Esquivel-Rodríguez, J; Xiong, Y; Han, X; et al. (30 May 2015). "Navigating 3D electron microscopy maps with EM-SURFER". BMC Bioinform. 16 (181). doi:10.1186/s12859-015-0580-6. PMC 4448178Freely accessible. PMID 26025554. 
  3. ^ Young, JY; Westbrook, JD; Feng, Z; Sala, R; Peisach, E; Oldfield, TJ; Sen, S; Gutmanas, A; Armstrong, DR; Berrisford, JM; Chen, L; Chen, M; Di Costanzo, L; Dimitropoulos, D; Gao, G; Ghosh, S; Gore, S; Guranovic, V; Hendrickx, PM; Hudson, BP; Igarashi, R; Ikegawa, Y; Kobayashi, N; Lawson, CL; Liang, Y; Mading, S; Mak, L; Mir, MS; Mukhopadhyay, A; Patwardhan, A; Persikova, I; Rinaldi, L; Sanz-Garcia, E; Sekharan, MR; Shao, C; Swaminathan, GJ; Tan, L; Ulrich, EL; van Ginkel, G; Yamashita, R; Yang, H; Zhuravleva, MA; Quesada, M; Kleywegt, GJ; Berman, HM; Markley, JL; Nakamura, H; Velankar, S; Burley, SK. "OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive". Structure. 25: 536–545. doi:10.1016/j.str.2017.01.004. PMC 5360273Freely accessible. PMID 28190782. 

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