EM Data Bank

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.^[2] As of 2015^[update], the resource contained over 2,600 entries with a mean resolution of 15Å.^[3]

EMDataBank.org

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	ebi.ac.uk/emdb

Deposition of data was originally via the EMdep deposition interface, but since 2016 deposition of data has been incorporated into the wwPDB OneDep interface.^[4]

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.

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]

See also

• Cryo-Electron Microscopy
• Colocalization Benchmark Source

References

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 3013769. PMID 20935055.
2. EMDB. "Electron Microscopy Data Bank". Electron Microscopy Data Bank. Retrieved 2021-08-05.
3. Esquivel-Rodríguez, J; Xiong, Y; Han, X; et al. (30 May 2015). "Navigating 3D electron microscopy maps with EM-SURFER". BMC Bioinform. 16 (181): 181. doi:10.1186/s12859-015-0580-6. PMC 4448178. PMID 26025554.
4. 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 (2017). "OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive". Structure. 25 (3): 536–545. doi:10.1016/j.str.2017.01.004. PMC 5360273. PMID 28190782.
5. Lawson, Catherine; Chiu, Wah, eds. (2018). "The CryoEM Structure Map and Model Challenges". Journal of Structural Biology. 204 (1). ISSN 1047-8477.

• 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. PMID 12417136.
• Fuller, Stephen D. (2003). "Depositing electron microscopy maps". Structure. 11 (1): 11–12. doi:10.1016/s0969-2126(02)00942-5. PMID 12517335.
• 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. PMID 14643225.
• 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. PMID 16043364.
• Tagari, M.; Tate, J.; Swaminathan, G. J.; et al. (2006). "E-MSD: improving data deposition and structure quality". Nucleic Acids Research. 34 (Database issue): 287–290. doi:10.1093/nar/gkj163. PMC 1347525. PMID 16381867.

External links

• Software tools for molecular microscopy
• EM Data Bank
• US and UK Search pages
• Japan Search page (EM Navigator in PDBj)